Test: mac.clang.python310.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20468」
Test files: 「file-system-view」 「file-list-view」
Daemon: hikaru-2     Started at: 2024-09-07 17:14:19     Run time: 0:07:34      State: failed

Failed sub-tests (click for more details):
T121_core.ResidueSelector

Test Log

Running: cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/python/PyRosetta && /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.10.clang/e318e4501985bbcdaf19d0cdceec7159/bin/python3.10 build.py -j24 --compiler clang --type MinSizeRel --python-include-dir=/Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.10.clang/e318e4501985bbcdaf19d0cdceec7159/include/python3.10 --python-lib=/Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.10.clang/e318e4501985bbcdaf19d0cdceec7159/lib Building PyRosetta MinSizeRel... Command line: cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/python/PyRosetta && /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.10.clang/e318e4501985bbcdaf19d0cdceec7159/bin/python3.10 build.py -j24 --compiler clang --type MinSizeRel --python-include-dir=/Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.10.clang/e318e4501985bbcdaf19d0cdceec7159/include/python3.10 --python-lib=/Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.10.clang/e318e4501985bbcdaf19d0cdceec7159/lib Creating PyRosetta in "MinSizeRel" mode in: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel Getting main repository root... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source && git rev-parse --show-toplevel /Volumes/scratch/b3.w/rosetta/commits/rosetta Updating Pybind11 Git submodule... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/.. && git submodule update --init -- source/external/pybind11 Updating Binder Git submodule... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/.. && git submodule update --init -- source/src/python/PyRosetta/binder LLVM:6.0.1 + Binder install is detected at /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.macOS-12.6-x86_64-i386-64bit.release, skipping LLVM installation and Binder building procedures... Updating compilation submodules, version, options and residue-type-enum files... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source && ./update_submodules.sh PyRosetta bcl zeromq && ./version.py && ./update_options.sh && ./update_ResidueType_enum_files.sh Updating submodules needed for compilation. Running versioning script ... Done. (0.2 seconds) Number of option files updated: 0 Total 4682 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed Generating bindings... cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/source/ && /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.macOS-12.6-x86_64-i386-64bit.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/source/ /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/source/all_rosetta_includes.hh -- -std=c++11 -isystem external -isystem external/include -isystem external/boost_submod -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -isystem external/rdkit -isystem external/bcl/include -Isrc -Isrc/platform/macos -isysroot `xcrun --show-sdk-path` -DPYROSETTA -DNOCRASHREPORT -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DUNUSUAL_ALLOCATOR_DECLARATION -DNDEBUG -DBCL_NO_OS_SIGNAL_HANDLING -DPYROSETTA_BINDER Process input file /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/source/all_rosetta_includes.hh Generate bindings, pass 1... Generate bindings, pass 2... ...truncated... protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.216 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.274 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.299 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for S┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Loop building -------------------------------------------------- FOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 mallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.252 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.273 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.273 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.191 577.191 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.295 577.191 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.306 577.191 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1086 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.306 577.191 protocols.moves.TrialCounter: repack trials= 6; accepts= 1.0000; energy_drop/trial= -50.02512 protocols.moves.TrialCounter: shear_ccd_min trials= 50; accepts= 0.8600; energy_drop/trial= -0.15222 protocols.moves.TrialCounter: small_ccd_min trials= 50; accepts= 0.8200; energy_drop/trial= -1.28296 Finished T660_LoopBuilding in 0:00:52.414121 C001_Carbohydrates_Demo01 - passed D010_Pose_structure - passed D020_Pose_scoring - passed D030_Fold_tree - passed D040_Movemap - passed D050_Packer_task - passed D060_Folding - passed D070_Refinement - passed D080_Loop_modeling - passed D090_Ala_scan - passed D100_Docking - passed D110_DNA_interface - passed D120_Ligand_interface - passed T000_Imports - passed T005_Bindings - passed T006_Options - passed T007_TracerIO - passed T008_Serialization - passed T009_Exceptions - passed T010_LoadPDB - passed T020_Pose_Bindings - passed T040_Types - passed T100_basic - passed T110_numeric - passed T120_core.RotamerSets - passed T150_PyMOL_Integration - passed T150_core.misc.lkball - passed T190_Bindings_Utility - passed T200_Scoring - passed T201_Scoring_pre_talaris - passed T220_AtomAtomPairEnergies - passed T250_Constraints - passed T300_PyJobDistributor - passed T400_Refinement - passed T500_Packing - passed T600_Docking - passed T650_LoopsKIC - passed T660_LoopBuilding - passed T700_FoldTree - passed T800_ClassicRelax - passed T850_SubClassing - passed T860_SubClassing_EnergyMethods - passed T870_SubClassing_EnergyMethods2 - passed T880_Other - passed T900_distributed - passed Workshop2test - passed Workshop3test - passed Workshop4test - passed Workshop5test - passed Workshop6test - passed Workshop7test - passed Workshop8test - passed Workshop9_my_shapes - passed Workshop9test - passed Following PyRosetta Tests FAILED: T121_core.ResidueSelector - FAILED

Sub-Tests Results

mac.clang.python310.PyRosetta.unit.T121_core.ResidueSelector 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git F. ====================================================================== FAIL: test_residue_selector_ctors (__main__.TestResidueSelectors) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T121_core.ResidueSelector.py", line 143, in test_residue_selector_ctors self.assertListEqual(selector_1.get_residues(pose), selector_2.get_residues(pose)) AssertionError: Lists differ: [1, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] != [2, 4, 6] First differing element 0: 1 2 First list contains 11 additional elements. First extra element 3: 7 - [1, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] + [2, 4, 6] ---------------------------------------------------------------------- Ran 2 tests in 10.199s FAILED (failures=1) Finished T121_core.ResidueSelector in 0:00:12.822412

mac.clang.python310.PyRosetta.unit.C001_Carbohydrates_Demo01 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git PDB file name: alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp Total residues: 3 Sequence: ZZZ Fold tree: FOLD_TREE EDGE 1 3 -1 PDB file name: alpha-D-Glcp-(1->6)-alpha-D-Glcp Total residues: 2 Sequence: ZZ Fold tree: FOLD_TREE EDGE 1 2 -1 PDB file name: beta-D-Galp-(1->4)-alpha-D-Glcp Total residues: 2 Sequence: ZZ Fold tree: FOLD_TREE EDGE 1 2 -1 alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp alpha-D-Glcp-(1->6)-alpha-D-Glcp beta-D-Galp-(1->4)-alpha-D-Glcp 1 ->4)-alpha-D-Glcp:reducing_end 2 ->4)-beta-D-Galp:non-reducing_end 1 ->4)-alpha-D-Glcp:reducing_end 2 ->4)-alpha-D-Glcp 3 ->4)-alpha-D-Glcp:non-reducing_end Residue 1: ->4)-alpha-D-Glcp:reducing_end:non-reducing_end (Glc, Z): Base: ->4)-alpha-D-Glcp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: glucose IUPAC Name: alpha-D-glucopyranose Abbreviation: alpha-D-Glcp Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: alpha Modifications: none Polymeric Information: Reducing?: yes Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : axial O2 : equatorial O3 : equatorial O4 : equatorial C6 : equatorial Atom Coordinates: C1 : 0, 0, 0 C2 : 1.55, 0, 0 C3 : 2.04812, 1.44664, 0 C4 : 1.50806, 2.11919, -1.26369 O4 : 1.94666, 3.46908, -1.30661 C5 : -0.0200415, 2.06186, -1.21358 O5 : -0.475077, 0.686176, -1.1593 VO5: -0.492509, 0.676579, -1.17187 (virtual) VC1: 0.031762, 0.00822503, 0.00564973 (virtual) O1 : -0.494034, 0.697555, 1.2082 O2 : 2.02401, -0.669275, 1.15922 O3 : 3.4779, 1.4716, 1.64563e-16 C6 : -0.614146, 2.71298, -2.43962 O6 : -0.225074, 4.07556, -2.53127 H1 : -0.370662, -1.03564, 0.00767336 H2 : 1.90812, -0.520035, -0.900727 H3 : 1.67301, 1.95456, 0.900727 H4 : 1.88381, 1.57916, -2.14527 HO4: 1.61609, 3.94572, -0.516717 H5 : -0.369153, 2.59396, -0.316372 HO1: -0.167832, 1.62167, 1.20877 HO2: 3.00401, -0.669275, 1.15922 HO3: 3.78886, 2.40096, 5.03844e-17 1H6 : -1.71106, 2.65811, -2.3783 2H6 : -0.261365, 2.17983, -3.33478 HO6: -0.621924, 4.47587, -3.33293 Mirrored relative to coordinates in ResidueType: FALSE Residue 1: ->4)-alpha-D-Galp:reducing_end:non-reducing_end (Gal, Z): Base: ->4)-alpha-D-Galp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: galactose IUPAC Name: alpha-D-galactopyranose Abbreviation: alpha-D-Galp Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: alpha Modifications: none Polymeric Information: Reducing?: yes Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : axial O2 : equatorial O3 : equatorial O4 : axial C6 : equatorial Atom Coordinates: C1 : 0, 0, 0 C2 : 1.55, 0, 0 C3 : 2.04812, 1.44664, 0 C4 : 1.50806, 2.11919, -1.26369 O4 : 1.98701, 1.42994, -2.4091 C5 : -0.0200415, 2.06186, -1.21358 O5 : -0.475077, 0.686176, -1.1593 VO5: -0.492509, 0.676579, -1.17187 (virtual) VC1: 0.031762, 0.00822503, 0.00564973 (virtual) O1 : -0.494034, 0.697555, 1.2082 O2 : 2.02401, -0.669275, 1.15922 O3 : 3.4779, 1.4716, 1.64563e-16 C6 : -0.614146, 2.71298, -2.43962 O6 : -0.225074, 4.07556, -2.53127 H1 : -0.370662, -1.03564, 0.00767336 H2 : 1.90812, -0.520035, -0.900727 H3 : 1.67301, 1.95456, 0.900727 H4 : 1.85245, 3.16359, -1.28863 HO4: 2.96665, 1.45445, -2.41977 H5 : -0.369153, 2.59396, -0.316372 HO1: -0.167832, 1.62167, 1.20877 HO2: 3.00401, -0.669275, 1.15922 HO3: 3.78886, 2.40096, 5.03844e-17 1H6 : -1.71106, 2.65811, -2.3783 2H6 : -0.261365, 2.17983, -3.33478 HO6: -0.621924, 4.47587, -3.33293 Mirrored relative to coordinates in ResidueType: FALSE Residue 1: ->3)-alpha-D-Manp:reducing_end:non-reducing_end (Man, Z): Base: ->3)-alpha-D-Manp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 O3 Backbone atoms: C1 C2 C3 O3 C4 C5 O5 VO5 VC1 H1 H2 H3 HO3 H4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O4 C6 O6 HO1 HO2 HO4 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: mannose IUPAC Name: alpha-D-mannopyranose Abbreviation: alpha-D-Manp Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: alpha Modifications: none Polymeric Information: Reducing?: yes Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : axial O2 : axial O3 : equatorial O4 : equatorial C6 : equatorial Atom Coordinates: C1 : 0, 0, 0 C2 : 1.55, 0, 0 C3 : 2.04812, 1.44664, 0 O3 : 3.4779, 1.4716, 1.64563e-16 C4 : 1.50806, 2.11919, -1.26369 C5 : -0.0200415, 2.06186, -1.21358 O5 : -0.475077, 0.686176, -1.1593 VO5: -0.492509, 0.676579, -1.17187 (virtual) VC1: 0.031762, 0.00822503, 0.00564973 (virtual) O1 : -0.494034, 0.697555, 1.2082 O2 : 2.02401, -0.669275, -1.15922 O4 : 1.94666, 3.46908, -1.30661 C6 : -0.614146, 2.71298, -2.43962 O6 : -0.225074, 4.07556, -2.53127 H1 : -0.370662, -1.03564, 0.00767336 H2 : 1.90812, -0.520035, 0.900727 H3 : 1.67301, 1.95456, 0.900727 HO3: 3.78886, 2.40096, 5.03844e-17 H4 : 1.88381, 1.57916, -2.14527 H5 : -0.369153, 2.59396, -0.316372 HO1: -0.167832, 1.62167, 1.20877 HO2: 3.00401, -0.669275, -1.15922 HO4: 1.61609, 3.94572, -0.516717 1H6 : -1.71106, 2.65811, -2.3783 2H6 : -0.261365, 2.17983, -3.33478 HO6: -0.621924, 4.47587, -3.33293 Mirrored relative to coordinates in ResidueType: FALSE 59.99999999999999 -59.99999999999999 60.00000000000001 -59.999999999999986 59.99999999999999 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 PDB file name: ../test/data/carbohydrates/Lex.pdb Total residues: 3 Sequence: ZZZ Fold tree: FOLD_TREE EDGE 1 2 -1 EDGE 1 3 -2 O3 C1 beta-D-Galp-(1->4)-beta-D-GlcpNAc alpha-L-Fucp- Residue 1: ->4)-beta-D-Glcp:reducing_end:->3)-branch:2-AcNH (Glc, Z): Base: ->4)-beta-D-Glcp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS BRANCH_POINT POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR C2_MODIFIED ACETYLAMINO_SUGAR Variant types: LOWER_TERMINUS_VARIANT C3_BRANCH_POINT C2_ACETYLAMINO_SUGAR Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO4 HO3 HO2 N2 CN2 CAN2 OCN2 HO1 1H6 2H6 HO6 HN2 1HC2 2HC2 3HC2 Branch-point atoms: O3 Carbohydrate Properties for this Residue: Basic Name: glucosamine IUPAC Name: ->4)-beta-2-(N-acetylamino)-2-deoxy-D-glucopyranose Abbreviation: ->4)-beta-D-GlcpNAc Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: beta Modifications: acetylamino sugar Polymeric Information: Reducing?: yes Main chain connection: (_->4) Branch connections: (_->3) Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : equatorial N2 : equatorial O3 : equatorial O4 : equatorial C6 : equatorial Atom Coordinates: C1 : 35.71, 122.693, 36.907 C2 : 36.264, 121.664, 35.887 C3 : 35.396, 120.362, 35.896 C4 : 35.215, 119.833, 37.36 O4 : 34.235, 118.792, 37.37 C5 : 34.756, 121.002, 38.316 O5 : 35.66, 122.104, 38.21 VO5: 35.66, 122.104, 38.21 (virtual) VC1: 35.7109, 122.617, 36.8656 (virtual) O1 : 36.369, 123.964, 36.94 O2 : 36.2371, 122.227, 34.5836 (virtual) O3 : 36.026, 119.359, 35.094 C6 : 34.689, 120.7, 39.82 O6 : 35.928, 120.224, 40.287 HO4: 34.615, 117.665, 38.155 (virtual) HO3: 35.546, 119.238, 33.75 (virtual) HO2: 36.5871, 121.577, 33.9392 (virtual) N2 : 36.245, 122.328, 34.583 CN2: 37.363, 122.3, 33.878 CAN2: 37.043, 123.112, 32.473 OCN2: 38.517, 122.472, 34.271 H1 : 34.6514, 122.845, 36.6496 H2 : 37.299, 121.411, 36.1601 H3 : 34.408, 120.587, 35.4681 H4 : 36.1743, 119.429, 37.7162 H5 : 33.7421, 121.32, 38.0316 HO1: 36.301, 124.391, 36.0604 1H6 : 33.9192, 119.935, 39.9976 2H6 : 34.4315, 121.623, 40.3596 HO6: 35.8659, 120.037, 41.247 HN2: 35.4316, 122.782, 34.2477 1HC2: 36.3241, 123.919, 32.671 2HC2: 36.5729, 122.428, 31.7525 3HC2: 37.9836, 123.478, 32.0377 Mirrored relative to coordinates in ResidueType: FALSE Residue 2: ->4)-beta-D-Galp:non-reducing_end (Gal, Z): Base: ->4)-beta-D-Galp Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR Variant types: UPPER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: galactose IUPAC Name: beta-D-galactopyranosyl Abbreviation: beta-D-Galp- Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: beta Modifications: none Polymeric Information: Reducing?: no Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O2 : equatorial O3 : equatorial O4 : axial C6 : equatorial Atom Coordinates: C1 : 34.615, 117.665, 38.155 C2 : 33.365, 116.921, 38.692 C3 : 33.836, 115.668, 39.463 C4 : 34.765, 114.785, 38.592 O4 : 33.936, 114.234, 37.591 C5 : 35.931, 115.629, 38.011 O5 : 35.406, 116.786, 37.348 VO5: 35.406, 116.786, 37.348 (virtual) VC1: 34.6528, 117.616, 38.2521 (virtual) O1 : 34.235, 118.792, 37.37 (virtual) O2 : 32.626, 117.74, 39.575 O3 : 32.706, 114.881, 39.893 C6 : 36.818, 114.855, 37.032 O6 : 37.611, 113.891, 37.692 HO1: 35.215, 119.833, 37.36 (virtual) H1 : 35.2209, 118.009, 39.0061 H2 : 32.7301, 116.628, 37.8427 H3 : 34.3885, 115.986, 40.3595 H4 : 35.1785, 113.978, 39.2143 HO4: 33.2273, 113.702, 38.0094 H5 : 36.5692, 115.975, 38.8375 HO2: 31.8431, 117.248, 39.8996 HO3: 33.0232, 114.092, 40.3795 1H6 : 37.4842, 115.562, 36.5164 2H6 : 36.1787, 114.34, 36.2998 HO6: 38.1635, 113.417, 37.0358 Mirrored relative to coordinates in ResidueType: FALSE Residue 3: ->4)-alpha-L-Fucp:non-reducing_end (Fuc, Z): Base: ->4)-alpha-L-Fucp Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE L_SUGAR PYRANOSE ALPHA_SUGAR C6_MODIFIED DEOXY_SUGAR Variant types: UPPER_TERMINUS_VARIANT C6_DEOXY_SUGAR Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO6 HO2 HO3 1H6 2H6 3H6 Carbohydrate Properties for this Residue: Basic Name: fucose IUPAC Name: alpha-L-fucopyranosyl Abbreviation: alpha-L-Fucp- Classification: aldohexose Stereochemistry: L Ring Form: pyranose Anomeric Form: alpha Modifications: deoxy sugar Polymeric Information: Reducing?: no Main chain connection: N/A Branch connections: none Ring Conformer: 1C4 (chair): C-P parameters (q, phi, theta): 0.55, 180, 180; nu angles (degrees): -60, 60, -60, 60, -60, 60 O2 : equatorial O3 : equatorial O4 : axial C6 : equatorial Atom Coordinates: C1 : 35.546, 119.238, 33.75 C2 : 36.615, 118.464, 32.939 C3 : 36.681, 116.991, 33.421 C4 : 35.284, 116.331, 33.366 O4 : 34.915, 116.247, 31.999 C5 : 34.24, 117.183, 34.142 O5 : 34.28, 118.546, 33.673 VO5: 34.28, 118.546, 33.673 (virtual) VC1: 35.5799, 119.134, 33.8691 (virtual) O1 : 36.026, 119.359, 35.094 (virtual) O2 : 37.839, 119.137, 33.073 O3 : 37.527, 116.202, 32.617 C6 : 32.809, 116.64, 34.044 O6 : 32.372, 116.598, 32.6936 (virtual) HO1: 35.396, 120.362, 35.896 (virtual) HO6: 31.4572, 116.249, 32.6565 (virtual) H1 : 35.3955, 120.244, 33.3315 H2 : 36.3437, 118.489, 31.8733 H3 : 37.0471, 116.97, 34.4581 H4 : 35.3419, 115.332, 33.8218 HO4: 34.8869, 117.147, 31.6118 H5 : 34.5158, 117.205, 35.2067 HO2: 38.5305, 118.662, 32.5661 HO3: 37.538, 115.283, 32.9572 1H6 : 32.7831, 115.622, 34.4596 2H6 : 32.137, 117.296, 34.6166 3H6 : 32.5045, 116.622, 32.9871 Mirrored relative to coordinates in ResidueType: FALSE PDB file name: ../test/data/carbohydrates/N-linked_14-mer_glycan.pdb Total residues: 19 Sequence: ANASAZZZZZZZZZZZZZZ Fold tree: FOLD_TREE EDGE 1 5 -1 EDGE 2 6 -2 ND2 C1 EDGE 6 14 -1 EDGE 8 15 -2 O6 C1 EDGE 15 17 -1 EDGE 15 18 -2 O6 C1 EDGE 18 19 -1 ANASA alpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-beta-D-GlcpNAc- alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-alpha-D-Manp- alpha-D-Manp-(1->2)-alpha-D-Manp- PDB file name: ../test/data/carbohydrates/O_glycan.pdb Total residues: 4 Sequence: ASAZ Fold tree: FOLD_TREE EDGE 1 3 -1 EDGE 2 4 -2 OG C1 ASA alpha-D-Glcp- core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -constant_seed -include_sugars -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.73307 seconds. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/maltotriose.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/isomaltose.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.Conformation: appending residue by a chemical bond in the foldtree: 3 ->4)-alpha-L-Fucp:non-reducing_end anchor: O3 1 root: C1 core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/Lex.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Gal2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Fuc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 3 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/N-linked_14-mer_glycan.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc6 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc7 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man8 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man9 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man10 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man11 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc12 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc13 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc14 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man15 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man16 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man17 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man18 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man19 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 6 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 15 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 18 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/O_glycan.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc4 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 4 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->4)-alpha-D-Glcp:non-reducing_end anchor: OG 2 root: C1 core.pose.carbohydrates.util: Glycosylated pose with a(n) Glcp-OGSER2 bond. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose.carbohydrates.util: Idealizing glycosidic torsions. core.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->3)-alpha-D-Galp:2-AcNH anchor: OG 2 root: C1 core.pose.carbohydrates.util: Glycosylated pose with a(n) a-D-GalpNAc-(1->3)-a-D-GalpNAc--OGSER2 bond. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose.carbohydrates.util: Idealizing glycosidic torsions. /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.core.pose import pose_from_saccharide_sequence /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:42: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for res in lactose: print( res.seqpos(), res.name() ) /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:43: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for res in maltotriose: print( res.seqpos(), res.name() ) /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:128: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for res in Lex: print( res ) Finished C001_Carbohydrates_Demo01 in 0:00:18.601279

mac.clang.python310.PyRosetta.unit.D010_Pose_structure 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ================================================================================ Loaded from ../test/data/test_in.pdb 116 residues 1 chain(s) ('A') Sequence: DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL Secondary Structure: LHHHHHHHHHHHHLLLLLLLLLHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHLLLLLLLLLLLLLL 63.7% Helical 0.0% Sheet 36.2% Loop ================================================================================ Pose numbered Residue 58 PDB numbered Residue 58 Single Letter: T Chain: A Secondary Structure: Helix Phi: -66.10647574201569 Psi: -37.61278973721056 Omega: 179.8787072171539 Chi 1: 157.77746590432227 Chi 2: 179.99312165369778 ================================================================================ core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.989654 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB protocols.DsspMover: LHHHHHHHHHHHHLLLLLLLLLHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHLLLLLLLLLLLLLL Finished D010_Pose_structure in 0:00:17.277707

mac.clang.python310.PyRosetta.unit.D020_Pose_scoring 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ================================================================================ ScoreFunction a: 949.3120641217009 ScoreFunction b: 949.3120641217009 ScoreFunction c: 54.59531500722412 ScoreFunction d: 54.59531500722412 ScoreFunction e: 639.6921382070861 ================================================================================ Loaded from ../test/data/test_in.pdb 116 residues Radius of Gyration ~ 15.070968422880075 Total Rosetta Score: 639.6921382070861 ================================================================================ Pose numbered Residue 58 Total Residue Score: 17.835676002501444 Score Breakdown: --------------------------------------------- fa_atr : -6.767255537709819 fa_rep : 18.770496833063742 fa_sol : 4.234940603509646 fa_intra_rep : 0.0152272562193792 fa_elec : -1.0892415802359439 pro_close : 0.0 hbond_sr_bb : 0.0 hbond_lr_bb : 0.0 hbond_bb_sc : 0.0 hbond_sc : 0.0 dslf_fa13 : 0.0 rama : -0.13507819308968252 omega : -0.006962209630289949 fa_dun : 3.0402048792529506 p_aa_pp : 0.043343951121461305 ref : -0.27 --------------------------------------------- Hydrogen bonds involving Residue 58: 58 H => 54 O |score: -0.9409534230157675 62 H => 58 O |score: -0.7406209609222881 ================================================================================ core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.9625 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.276951 seconds to load from binary core.scoring.ScoreFunction: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.800 -715.300 -572.240 fa_rep 0.440 827.739 364.205 fa_sol 0.750 504.855 378.642 fa_intra_rep 0.004 563.466 2.254 fa_elec 0.700 -133.742 -93.619 pro_close 1.000 17.220 17.220 hbond_sr_bb 1.170 -47.398 -55.455 hbond_lr_bb 1.170 -0.785 -0.918 hbond_bb_sc 1.170 -5.673 -6.637 hbond_sc 1.100 -1.540 -1.693 dslf_fa13 1.000 0.000 0.000 rama 0.200 4.872 0.974 omega 0.500 16.053 8.026 fa_dun 0.560 1133.922 634.996 p_aa_pp 0.320 -17.819 -5.702 ref 1.000 -30.360 -30.360 --------------------------------------------------- Total weighted score: 639.692 Finished D020_Pose_scoring in 0:00:19.981126

mac.clang.python310.PyRosetta.unit.D030_Fold_tree 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git The first FoldTree is proper: True The second FoldTree is proper: True linearized structure output pre jump perturbed structure output first internal jump edge perturbed structure output second internal jump edge perturbed structure output post jump perturbed structure output core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.05345 seconds. Finished D030_Fold_tree in 0:00:17.101115

mac.clang.python310.PyRosetta.unit.D040_Movemap 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.08629 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB resnum BB CHI NU BRANCH 001 TRUE FALSE FALSE FALSE 002 TRUE FALSE FALSE FALSE 003 TRUE FALSE FALSE FALSE 004 TRUE FALSE FALSE FALSE 005 TRUE FALSE FALSE FALSE 006 TRUE FALSE FALSE FALSE 007 TRUE FALSE FALSE FALSE 008 TRUE FALSE FALSE FALSE 009 TRUE FALSE FALSE FALSE 010 TRUE FALSE FALSE FALSE 011 TRUE FALSE FALSE FALSE 012 TRUE FALSE FALSE FALSE 013 TRUE FALSE FALSE FALSE 014 TRUE FALSE FALSE FALSE 015 TRUE FALSE FALSE FALSE 016 TRUE FALSE FALSE FALSE 017 TRUE FALSE FALSE FALSE 018 TRUE FALSE FALSE FALSE 019 TRUE FALSE FALSE FALSE 020 TRUE FALSE FALSE FALSE 021 TRUE FALSE FALSE FALSE 022 TRUE FALSE FALSE FALSE 023 TRUE FALSE FALSE FALSE 024 TRUE FALSE FALSE FALSE 025 TRUE FALSE FALSE FALSE 026 TRUE FALSE FALSE FALSE 027 TRUE FALSE FALSE FALSE 028 TRUE FALSE FALSE FALSE 029 TRUE FALSE FALSE FALSE 030 TRUE FALSE FALSE FALSE 031 TRUE FALSE FALSE FALSE 032 TRUE FALSE FALSE FALSE 033 TRUE FALSE FALSE FALSE 034 TRUE FALSE FALSE FALSE 035 TRUE FALSE FALSE FALSE 036 TRUE FALSE FALSE FALSE 037 TRUE FALSE FALSE FALSE 038 TRUE FALSE FALSE FALSE 039 TRUE FALSE FALSE FALSE 040 TRUE FALSE FALSE FALSE 041 TRUE FALSE FALSE FALSE 042 TRUE FALSE FALSE FALSE 043 TRUE FALSE FALSE FALSE 044 TRUE FALSE FALSE FALSE 045 TRUE FALSE FALSE FALSE 046 TRUE FALSE FALSE FALSE 047 TRUE FALSE FALSE FALSE 048 TRUE FALSE FALSE FALSE 049 TRUE FALSE FALSE FALSE 050 TRUE FALSE FALSE FALSE 051 TRUE FALSE FALSE FALSE 052 TRUE FALSE FALSE FALSE 053 TRUE FALSE FALSE FALSE 054 TRUE FALSE FALSE FALSE 055 TRUE FALSE FALSE FALSE 056 TRUE FALSE FALSE FALSE 057 TRUE FALSE FALSE FALSE 058 TRUE FALSE FALSE FALSE 059 TRUE FALSE FALSE FALSE 060 TRUE FALSE FALSE FALSE 061 TRUE FALSE FALSE FALSE 062 TRUE FALSE FALSE FALSE 063 TRUE FALSE FALSE FALSE 064 TRUE FALSE FALSE FALSE 065 TRUE FALSE FALSE FALSE 066 TRUE FALSE FALSE FALSE 067 TRUE FALSE FALSE FALSE 068 TRUE FALSE FALSE FALSE 069 TRUE FALSE FALSE FALSE 070 TRUE FALSE FALSE FALSE 071 TRUE FALSE FALSE FALSE 072 TRUE FALSE FALSE FALSE 073 TRUE FALSE FALSE FALSE 074 TRUE FALSE FALSE FALSE 075 TRUE FALSE FALSE FALSE 076 TRUE FALSE FALSE FALSE 077 TRUE FALSE FALSE FALSE 078 TRUE FALSE FALSE FALSE 079 TRUE FALSE FALSE FALSE 080 TRUE FALSE FALSE FALSE 081 TRUE FALSE FALSE FALSE 082 TRUE FALSE FALSE FALSE 083 TRUE FALSE FALSE FALSE 084 TRUE FALSE FALSE FALSE 085 TRUE FALSE FALSE FALSE 086 TRUE FALSE FALSE FALSE 087 TRUE FALSE FALSE FALSE 088 TRUE FALSE FALSE FALSE 089 TRUE FALSE FALSE FALSE 090 TRUE FALSE FALSE FALSE 091 TRUE FALSE FALSE FALSE 092 TRUE FALSE FALSE FALSE 093 TRUE FALSE FALSE FALSE 094 TRUE FALSE FALSE FALSE 095 TRUE FALSE FALSE FALSE 096 TRUE FALSE FALSE FALSE 097 TRUE FALSE FALSE FALSE 098 TRUE FALSE FALSE FALSE 099 TRUE FALSE FALSE FALSE 100 TRUE FALSE FALSE FALSE 101 TRUE FALSE FALSE FALSE 102 TRUE FALSE FALSE FALSE 103 TRUE FALSE FALSE FALSE 104 TRUE FALSE FALSE FALSE 105 TRUE FALSE FALSE FALSE 106 TRUE FALSE FALSE FALSE 107 TRUE FALSE FALSE FALSE 108 TRUE FALSE FALSE FALSE 109 TRUE FALSE FALSE FALSE 110 TRUE FALSE FALSE FALSE 111 TRUE FALSE FALSE FALSE 112 TRUE FALSE FALSE FALSE 113 TRUE FALSE FALSE FALSE 114 TRUE FALSE FALSE FALSE 115 TRUE FALSE FALSE FALSE 116 TRUE FALSE FALSE FALSE ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Pre minimization score: 949.3120641217009 Post minimization score: 699.8780157437467 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.271517 seconds to load from binary Finished D040_Movemap in 0:00:21.149679

mac.clang.python310.PyRosetta.unit.D050_Packer_task 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 TRUE FALSE ASP:NtermProteinFull 2 TRUE FALSE ALA 3 TRUE FALSE ILE 4 TRUE FALSE THR 5 TRUE FALSE ILE 6 TRUE FALSE HIS,HIS_D 7 TRUE FALSE SER 8 TRUE FALSE ILE 9 TRUE FALSE LEU 10 TRUE FALSE ASP 11 TRUE FALSE TRP 12 TRUE FALSE ILE 13 TRUE FALSE GLU 14 TRUE FALSE ASP 15 TRUE FALSE ASN 16 TRUE FALSE LEU 17 TRUE FALSE GLU 18 TRUE FALSE SER 19 TRUE FALSE PRO 20 TRUE FALSE LEU 21 TRUE FALSE SER 22 TRUE FALSE LEU 23 TRUE FALSE GLU 24 TRUE FALSE LYS 25 TRUE FALSE VAL 26 TRUE FALSE SER 27 TRUE FALSE GLU 28 TRUE FALSE ARG 29 TRUE FALSE SER 30 TRUE FALSE GLY 31 TRUE FALSE TYR 32 TRUE FALSE SER 33 TRUE FALSE LYS 34 TRUE FALSE TRP 35 TRUE FALSE HIS,HIS_D 36 TRUE FALSE LEU 37 TRUE FALSE GLN 38 TRUE FALSE ARG 39 TRUE FALSE MET 40 TRUE FALSE PHE 41 TRUE FALSE LYS 42 TRUE FALSE LYS 43 TRUE FALSE GLU 44 TRUE FALSE THR 45 TRUE FALSE GLY 46 TRUE FALSE HIS,HIS_D 47 TRUE FALSE SER 48 TRUE FALSE LEU 49 TRUE FALSE GLY 50 TRUE FALSE GLN 51 TRUE FALSE TYR 52 TRUE FALSE ILE 53 TRUE FALSE ARG 54 TRUE FALSE SER 55 TRUE FALSE ARG 56 TRUE FALSE LYS 57 TRUE FALSE MET 58 TRUE FALSE THR 59 TRUE FALSE GLU 60 TRUE FALSE ILE 61 TRUE FALSE ALA 62 TRUE FALSE GLN 63 TRUE FALSE LYS 64 TRUE FALSE LEU 65 TRUE FALSE LYS 66 TRUE FALSE GLU 67 TRUE FALSE SER 68 TRUE FALSE ASN 69 TRUE FALSE GLU 70 TRUE FALSE PRO 71 TRUE FALSE ILE 72 TRUE FALSE LEU 73 TRUE FALSE TYR 74 TRUE FALSE LEU 75 TRUE FALSE ALA 76 TRUE FALSE GLU 77 TRUE FALSE ARG 78 TRUE FALSE TYR 79 TRUE FALSE GLY 80 TRUE FALSE PHE 81 TRUE FALSE GLU 82 TRUE FALSE SER 83 TRUE FALSE GLN 84 TRUE FALSE GLN 85 TRUE FALSE THR 86 TRUE FALSE LEU 87 TRUE FALSE THR 88 TRUE FALSE ARG 89 TRUE FALSE THR 90 TRUE FALSE PHE 91 TRUE FALSE LYS 92 TRUE FALSE ASN 93 TRUE FALSE TYR 94 TRUE FALSE PHE 95 TRUE FALSE ASP 96 TRUE FALSE VAL 97 TRUE FALSE PRO 98 TRUE FALSE PRO 99 TRUE FALSE HIS,HIS_D 100 TRUE FALSE LYS 101 TRUE FALSE TYR 102 TRUE FALSE ARG 103 TRUE FALSE MET 104 TRUE FALSE THR 105 TRUE FALSE ASN 106 TRUE FALSE MET 107 TRUE FALSE GLN 108 TRUE FALSE GLY 109 TRUE FALSE GLU 110 TRUE FALSE SER 111 TRUE FALSE ARG 112 TRUE FALSE PHE 113 TRUE FALSE LEU 114 TRUE FALSE HIS,HIS_D 115 TRUE FALSE PRO 116 TRUE FALSE LEU:CtermProteinFull Pre packing score: 949.3120641217009 Post packing score: 119.97075192647779 #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 FALSE FALSE 2 FALSE FALSE 3 FALSE FALSE 4 FALSE FALSE 5 FALSE FALSE 6 FALSE FALSE 7 FALSE FALSE 8 FALSE FALSE 9 FALSE FALSE 10 FALSE FALSE 11 FALSE FALSE 12 FALSE FALSE 13 FALSE FALSE 14 FALSE FALSE 15 FALSE FALSE 16 FALSE FALSE 17 FALSE FALSE 18 FALSE FALSE 19 FALSE FALSE 20 FALSE FALSE 21 FALSE FALSE 22 FALSE FALSE 23 FALSE FALSE 24 FALSE FALSE 25 FALSE FALSE 26 FALSE FALSE 27 FALSE FALSE 28 FALSE FALSE 29 FALSE FALSE 30 FALSE FALSE 31 FALSE FALSE 32 FALSE FALSE 33 FALSE FALSE 34 FALSE FALSE 35 FALSE FALSE 36 FALSE FALSE 37 FALSE FALSE 38 FALSE FALSE 39 FALSE FALSE 40 FALSE FALSE 41 FALSE FALSE 42 FALSE FALSE 43 FALSE FALSE 44 FALSE FALSE 45 FALSE FALSE 46 FALSE FALSE 47 FALSE FALSE 48 FALSE FALSE 49 FALSE FALSE 50 FALSE FALSE 51 FALSE FALSE 52 FALSE FALSE 53 FALSE FALSE 54 FALSE FALSE 55 FALSE FALSE 56 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 57 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 58 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 59 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 60 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 61 FALSE FALSE 62 FALSE FALSE 63 FALSE FALSE 64 FALSE FALSE 65 FALSE FALSE 66 FALSE FALSE 67 FALSE FALSE 68 FALSE FALSE 69 FALSE FALSE 70 FALSE FALSE 71 FALSE FALSE 72 FALSE FALSE 73 FALSE FALSE 74 FALSE FALSE 75 FALSE FALSE 76 FALSE FALSE 77 FALSE FALSE 78 FALSE FALSE 79 FALSE FALSE 80 FALSE FALSE 81 FALSE FALSE 82 FALSE FALSE 83 FALSE FALSE 84 FALSE FALSE 85 FALSE FALSE 86 FALSE FALSE 87 FALSE FALSE 88 FALSE FALSE 89 FALSE FALSE 90 FALSE FALSE 91 FALSE FALSE 92 FALSE FALSE 93 FALSE FALSE 94 FALSE FALSE 95 FALSE FALSE 96 FALSE FALSE 97 FALSE FALSE 98 FALSE FALSE 99 FALSE FALSE 100 FALSE FALSE 101 FALSE FALSE 102 FALSE FALSE 103 FALSE FALSE 104 FALSE FALSE 105 FALSE FALSE 106 FALSE FALSE 107 FALSE FALSE 108 FALSE FALSE 109 FALSE FALSE 110 FALSE FALSE 111 FALSE FALSE 112 FALSE FALSE 113 FALSE FALSE 114 FALSE FALSE 115 FALSE FALSE 116 FALSE FALSE Design with all proteogenic amino acids at (pose numbered) residues 56 to 60 Pre-design score: 949.3120641217009 Pre-design sequence: ...SRKMTEIAQ... Post-design score: 880.7910264455371 Post-design sequence: ...SRIATEIAQ... core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.0745 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.223287 seconds to load from binary core.pack.pack_rotamers: built 3014 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1684 rotamers at 5 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph Finished D050_Packer_task in 0:00:24.779935

mac.clang.python310.PyRosetta.unit.D060_Folding 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Working on decoy: fold_output_0.pdb ================================================================================ Potential Disulfides: ================================================================================ ===== Centroid Scores ===== Original Score : 445.27957490489933 fold_output_1 : 131.88750967868828 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.995886 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.029318 seconds. core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.245219 seconds to load from binary Finished D060_Folding in 0:00:21.158163

mac.clang.python310.PyRosetta.unit.D070_Refinement 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Working on decoy: refine_output_0.pdb Original Score : 949.3120641217009 refine_output_1 : -161.54772503563524 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.932208 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.283477 seconds to load from binary core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.pack.pack_rotamers: built 3108 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3310 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3312 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3206 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3281 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3262 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3252 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3292 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 3375 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph Finished D070_Refinement in 0:00:50.150681

mac.clang.python310.PyRosetta.unit.D080_Loop_modeling 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -run:jran 1111125 -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111125 seed_offset=0 real_seed=1111125 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111125 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.945388 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB protocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 14 -1 EDGE 14 17 -1 EDGE 14 20 1 EDGE 20 18 -1 EDGE 20 116 -1 protocols.loops.loops_main: Added cutpoint variant to residue 17 protocols.loops.loops_main: Added cutpoint variant to residue 18 core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.029018 seconds. basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.286346 seconds to load from binary core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.pack.pack_rotamers: built 1795 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.loops.loops_main: Added cutpoint variant to residue 17 protocols.loops.loops_main: Added cutpoint variant to residue 18 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 825 rotamers at 28 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 138.566 138.566 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 1 138.566 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5737 74.5737 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 70.5721 70.5721 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.7059 62.7059 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.0896 61.0896 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 59.9574 59.9574 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 59.7899 59.7899 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 56.1949 56.1949 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.878 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9522 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9578 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.0426 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 57.9858 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 56.0656 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.6881 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.0689 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.1019 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9445 54.878 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.8568 54.8568 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.2267 54.8568 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.8908 54.8568 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 783 rotamers at 25 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.3263 54.3263 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 2 62.6631 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8803 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8753 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9224 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8885 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8894 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8576 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9176 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.7747 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5236 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9741 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9114 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8428 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8527 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5602 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5602 61.5112 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 796 rotamers at 25 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.3972 61.3972 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 3 66.3631 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 66.3631 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 66.3631 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 66.3631 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3767 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4066 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3734 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3549 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3995 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.7208 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.6825 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4082 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3799 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4224 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.365 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3398 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4835 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.2987 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3489 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3349 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.2569 66.3631 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 795 rotamers at 25 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 65.9596 65.9596 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 4 69.5649 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.2748 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3856 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.58 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3005 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3036 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3259 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.4736 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.2659 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.2677 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3206 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.291 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.4704 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.268 69.5649 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 794 rotamers at 25 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 68.7119 68.7119 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 5 71.0257 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 71.0257 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 71.0257 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.7812 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5137 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5396 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5293 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5465 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5153 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5033 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.4984 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5009 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5585 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 7/10 protocols.loops.loop_mover.refine.LoopRefin┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Working on decoy: loop_output_0.pdb eInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5506 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5025 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5046 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5405 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.7434 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5965 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5456 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5932 71.0257 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 794 rotamers at 25 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 71.4655 71.0257 protocols.moves.TrialCounter: repack trials= 6; accepts= 1.0000; energy_drop/trial= -2.36900 protocols.moves.TrialCounter: shear_ccd_min trials= 50; accepts= 0.8400; energy_drop/trial= 0.09451 protocols.moves.TrialCounter: small_ccd_min trials= 50; accepts= 0.8200; energy_drop/trial= -1.58677 /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/demo/D080_Loop_modeling.py:131: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.protocols.loops.loop_mover.refine import LoopMover_Refine_CCD Finished D080_Loop_modeling in 0:01:05.203697

mac.clang.python310.PyRosetta.unit.D090_Ala_scan 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.05159 seconds. core.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34 core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1 core.conformation.Conformation: Found disulfide between residues 1 119 core.conformation.Conformation: Found disulfide between residues 40 56 core.conformation.Conformation: Found disulfide between residues 133 194 core.conformation.Conformation: Found disulfide between residues 161 175 core.conformation.Conformation: Found disulfide between residues 184 213 core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.276329 seconds to load from binary core.pack.pack_rotamers: built 238 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 180 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 189 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 176 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 185 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 463 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 481 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 374 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 392 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 253 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 288 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 222 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 244 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 382 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 403 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 382 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 403 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 761 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 769 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 761 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 769 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 661 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 701 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 583 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 623 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 479 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 487 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 479 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 487 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 450 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 477 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 442 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 469 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 400 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 422 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 494 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 516 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 193 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 217 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 165 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 189 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 115 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 123 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 62 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 70 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 184 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 185 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 160 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 160 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 152 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 175 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 86 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 109 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 694 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 694 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 378 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 378 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 451 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 476 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 451 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 476 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 271 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 306 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 241 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 262 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 334 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 369 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 388 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 423 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 573 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 598 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 543 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 560 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 837 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 877 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 676 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 716 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 675 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 688 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 453 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 466 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 747 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 747 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 745 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 745 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 643 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 675 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 482 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 514 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 551 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 578 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 514 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 513 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 860 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 916 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 866 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 868 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 819 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 819 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 658 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 658 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 512 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 620 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 405 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 513 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 491 rotamers at 6 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 491 rotamers at 6 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 438 rotamers at 6 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 438 rotamers at 6 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 457 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 485 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 454 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 482 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 377 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 377 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 373 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 373 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 349 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 295 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 331 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 277 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 430 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 538 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 168 rotamers at 5 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 276 rotamers at 5 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 217 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 325 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 164 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 164 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 509 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 638 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 490 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 600 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 289 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 453 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 287 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 451 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 523 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 563 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 416 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 456 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 629 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 723 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 634 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 733 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 460 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 492 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 426 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 450 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 420 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 468 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 414 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 454 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInte┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ================================================================================ Trial 1 Mutants (PDB numbered) "ddG" (interaction dependent score change) F39A 0.3037419927867404 H40A 0.062291291501423984 F41A -0.5179182491857546 C42A 0.0 A55A 0.7526408562278846 H57A -1.8773173484200072 C58A -0.2193728458406099 I99A 0.8234264858139682 G142A 0.010933632634589685 L143A 1.3741232149200755 T151A 0.43839262942344703 W172A 1.0909707675280913 K175A -0.17668088813627492 S190A -0.43304128739850967 C191A 0.0 M192A -0.3059494545528878 G193A -1.0066840572941373 D194A 0.7375507270811852 S195A -3.072403605789475 G196A -0.656357391887866 V213A 0.5586573712038216 S214A -1.1522661010514526 W215A -1.109766942631154 G216A -1.4328724668491475 S217A -0.3300597192764201 S218A -3.1289141356602954 T219A -0.158856433434579 V227A -0.14919286885873362 L37A -0.0781716063218596 E39A -0.2842576324852075 G40A -0.35176205410326133 S41A -0.32954428119910517 P42A 1.3097229786820321 V43A 1.5310898301999032 T44A -1.7214007763273287 L45A 0.8101922525750069 D46A -4.459550972237139 L47A 0.7556054312547076 R48A -0.5921687568389871 Y49A -1.1555400302177077 R53A -0.02278040179214713 F55A -1.3537481969085547 G70A 0.04813369810437962 ================================================================================ Likely Hotspot Residues H57A L143A W172A S195A S218A P42A V43A T44A D46A ================================================================================ ractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 179 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 212 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 82 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 113 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 136 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 148 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 127 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 139 rotamers at 8 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 285 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 285 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 194 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 194 rotamers at 12 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 407 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 353 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 372 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 318 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 170 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 210 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 188 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 228 rotamers at 11 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/demo/D090_Ala_scan.py:84: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.protocols.scoring import Interface Finished D090_Ala_scan in 0:00:50.520282

mac.clang.python310.PyRosetta.unit.D100_Docking 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.951995 seconds. core.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34 core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1 core.conformation.Conformation: Found disulfide between residues 1 119 core.conformation.Conformation: Found disulfide between residues 40 56 core.conformation.Conformation: Found disulfide between residues 133 194 core.conformation.Conformation: Found disulfide between residues 161 175 core.conformation.Conformation: Found disulfide between residues 184 213 core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.284328 seconds to load from binary core.pack.pack_rotamers: built 238 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.029844 seconds. basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: Reading options... core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.moves.RigidBodyMover: Randomize: Jump (before): RT -0.43256 0.815075 -0.385415 -0.869462 -0.490229 -0.0609182 -0.238594 0.308753 0.92073 -20.1643 -14.8001 1.00855 protocols.moves.RigidBodyMover: Randomize: Rot. Center (before): 7.27132 -0.353633 18.2062 protocols.geometry.RB_geometry: random_reorientation_matrix phi: 99.6306 psi: 274.195 theta: 88.635 protocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.501566 0.0943906 -0.859955 -0.450893 -0.819823 -0.352967 -0.738328 0.564784 -0.368635 1.19304 -6.08076 -26.9467 protocols.moves.RigidBodyMover: Randomize: Rot. Center (after): 7.27132 -0.353633 18.2062 protocols.moves.RigidBodyMover: Randomize: --- protocols.moves.RigidBodyMover: Randomize: Jump (before): RT 0.501566 0.0943906 -0.859955 -0.450893 -0.819823 -0.352967 -0.738328 0.564784 -0.368635 1.19304 -6.08076 -26.9467 protocols.moves.RigidBodyMover: Randomize: Rot. Center (before): 14.3539 25.5364 12.8647 protocols.geometry.RB_geometry: random_reorientation_matrix phi: 168.165 psi: 253.962 theta: 126.406 protocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.90194 0.265425 -0.340666 0.355013 -0.00652657 0.934839 0.245906 -0.964109 -0.100116 3.28027 -14.8952 32.2801 protocols.moves.RigidBodyMover: Randomize: Rot. Center (after): 26.3065 0.818941 -13.1763 protocols.moves.RigidBodyMover: Randomize: --- protocols.moves.RigidBodyMover: Spin: Jump (before): RT 0.904505 0.256377 -0.340796 0.348103 0.017797 0.937287 0.246364 -0.966413 -0.0731481 7.43102 0.0211541 38.4478 protocols.moves.RigidBodyMover: Spin: Rot (before): 15.2576 -9.26054 -20.5784 protocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.96652 0.250828 -0.0540836 0.0814818 -0.10016 0.991629 0.243312 -0.962836 -0.117244 6.83388 -0.112006 38.5401 protocols.moves.RigidBodyMover: Spin: Rot (after): 15.2576 -9.26054 -20.5784 protocols.moves.RigidBodyMover: Spin: --- protocols.docking.DockingInitialPerturbation: sliding into contact protocols.docking.DockingInitialPerturbation: Moving away protocols.docking.DockingInitialPerturbation: Moving together basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor! protocols.docking.DockingProtocol: Setting docking foldtree protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 protocols.docking.DockingProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: /// /// protocols.docking.DockingProtocol: /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: /// High Resolution Filter: on /// protocols.docking.DockingProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 protocols.docking.DockingInitialPerturbation: sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: sliding into contact protocols.docking.DockingInitialPerturbation: Moving away protocols.docking.DockingInitialPerturbation: Moving together protocols.docking.DockingProtocol: finished initial perturbation protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Acceptance rate is: 0.32 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.1 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.1 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.14 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.14 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 4 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 8 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 9 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 10 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 11 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 13 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 14 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 15 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 16 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 19 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 20 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 21 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 22 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 24 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 25 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 26 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 27 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 28 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 29 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 30 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 31 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 32 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 33 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 35 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 37 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 38 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 39 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 40 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 43 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 44 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 45 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 46 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 47 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 48 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 49 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 50 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 51 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 52 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 53 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 54 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 55 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 56 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 58 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 59 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 60 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 61 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 62 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 63 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 64 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 66 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 68 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 69 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 70 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 71 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 73 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 74 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 75 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 77 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 78 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 79 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 80 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 81 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 82 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 83 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 85 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 86 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 87 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 88 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 89 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 91 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 92 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 93 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 94 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 95 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 96 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 97 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 98 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 99 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 100 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 101 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 103 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 104 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 105 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 106 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 107 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 108 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 110 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 112 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 114 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 115 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 116 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 117 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 118 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 119 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 120 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 121 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 122 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 123 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 124 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 125 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 126 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 127 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 128 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 129 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 131 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 132 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 133 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 134 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 135 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 136 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 138 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 141 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 143 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 144 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 145 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 146 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 148 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 149 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 150 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 151 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 152 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 153 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 154 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 155 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 156 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 157 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 158 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 159 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 160 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 161 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 165 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 167 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 168 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 169 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 170 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 171 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 172 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 173 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 174 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 175 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 176 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 178 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 179 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 181 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 182 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 183 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 184 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 185 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 187 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 188 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 191 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 192 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 193 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 194 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 195 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 197 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 199 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 200 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 201 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 202 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 203 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 205 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 206 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 207 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 208 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 210 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 211 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 212 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 213 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 215 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 216 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 217 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 218 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 221 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 222 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 223 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 224 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 225 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 226 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 227 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 228 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 229 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 230 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 231 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 234 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 235 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 236 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 237 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 238 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 240 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 241 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 242 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 243 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 244 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 245 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 248 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 249 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 250 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 251 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 252 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 253 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 254 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 255 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 256 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 257 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 258 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 260 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 261 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 262 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 263 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 264 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 265 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 266 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 267 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 268 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 269 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 270 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 273 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 274 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 275 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 276 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 277 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 278 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 279 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 282 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 283 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 284 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 285 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 287 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 289 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 291 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 292 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 293 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 294 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 295 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 296 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 297 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 298 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 299 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 300 because of missing atom number 5 atom name CB core.pack.pack_rotamers: built 7982 rotamers at 274 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: Score before repack: protocols.docking.DockingProtocol: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.338 -1751.322 -591.947 fa_rep 0.186 8417.226 1562.910 fa_sol 0.242 975.051 235.962 fa_elec 0.026 -338.684 -8.806 fa_pair 0.164 -33.981 -5.573 hbond_sr_bb 0.245 -47.347 -11.600 hbond_lr_bb 0.245 -100.043 -24.511 hbond_bb_sc 0.245 -24.902 -6.101 hbond_sc 0.245 -6.857 -1.680 dslf_ss_dst 0.500 -15.294 -7.647 dslf_cs_ang 2.000 1.100 2.200 dslf_ss_dih 5.000 0.462 2.308 dslf_ca_dih 5.000 0.254 1.269 fa_dun 0.036 1557.509 56.070 --------------------------------------------------- Total weighted score: 1202.856 core.pack.pack_rotamers: built 4094 rotamers at 291 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: Score after repack: protocols.docking.DockingProtocol: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.338 -1690.551 -571.406 fa_rep 0.186 3035.584 563.647 fa_sol 0.242 913.492 221.065 fa_elec 0.026 -353.527 -9.192 fa_pair 0.164 -37.809 -6.201 hbond_sr_bb 0.245 -47.347 -11.600 hbond_lr_bb 0.245 -100.043 -24.511 hbond_bb_sc 0.245 -26.342 -6.454 hbond_sc 0.245 -8.149 -1.996 dslf_ss_dst 0.500 -15.294 -7.647 dslf_cs_ang 2.000 1.100 2.200 dslf_ss_dih 5.000 0.462 2.308 dslf_ca_dih 5.000 0.254 1.269 fa_dun 0.036 667.709 24.038 --------------------------------------------------- Total weighted score: 175.521 protocols.docking.DockMCMProtocol: in DockMCMProtocol.apply protocols.docking.DockMCMProtocol: Using the DockingTaskFactory. protocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockMCMCycle: /// Dockable Jumps: 1 /// protocols.docking.DockMCMCycle: /// Translation: 0.1 /// protocols.docking.DockMCMCycle: /// Rotation: 5 /// protocols.docking.DockMCMCycle: /// Scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.338) (fa_rep 0.18568) (fa_sol 0.242) (fa_elec 0.026) (fa_pair 0.164) (hbond_sr_bb 0.245) (hbond_lr_bb 0.245) (hbond_bb_sc 0.245) (hbond_sc 0.245) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.036) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.338) (fa_rep 0.18568) (fa_sol 0.242) (fa_elec 0.026) (fa_pair 0.164) (hbond_sr_bb 0.245) (hbond_lr_bb 0.245) (hbond_bb_sc 0.245) (hbond_sc 0.245) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.036) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hb┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Working on decoy: dock_output_0.pdb onds: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1214 rotamers at 38 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 423 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 651 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 785 rotamers at 24 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 940 rotamers at 26 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 841 rotamers at 22 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.docking.DockingProtocol.metrics: unbound pose: protocols.docking.DockingProtocol.metrics: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -1625.788 -1625.788 fa_rep 0.550 635.971 349.784 fa_sol 1.000 858.723 858.723 fa_intra_rep 0.005 774.341 3.872 fa_intra_sol_xover4 1.000 50.611 50.611 lk_ball_wtd 1.000 -37.926 -37.926 fa_elec 1.000 -348.335 -348.335 pro_close 1.250 102.522 128.153 hbond_sr_bb 1.000 -47.347 -47.347 hbond_lr_bb 1.000 -100.043 -100.043 hbond_bb_sc 1.000 -36.544 -36.544 hbond_sc 1.000 -10.049 -10.049 dslf_fa13 1.250 -4.134 -5.168 omega 0.400 32.147 12.859 fa_dun 0.700 663.521 464.465 p_aa_pp 0.600 -69.949 -41.970 yhh_planarity 0.625 0.000 0.000 ref 1.000 170.937 170.937 rama_prepro 0.450 69.289 31.180 --------------------------------------------------- Total weighted score: -182.585 protocols.docking.DockingProtocol.metrics: bound pose: protocols.docking.DockingProtocol.metrics: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -1645.760 -1645.760 fa_rep 0.550 640.173 352.095 fa_sol 1.000 871.823 871.823 fa_intra_rep 0.005 774.341 3.872 fa_intra_sol_xover4 1.000 50.611 50.611 lk_ball_wtd 1.000 -38.003 -38.003 fa_elec 1.000 -348.063 -348.063 pro_close 1.250 102.522 128.153 hbond_sr_bb 1.000 -47.347 -47.347 hbond_lr_bb 1.000 -100.043 -100.043 hbond_bb_sc 1.000 -36.544 -36.544 hbond_sc 1.000 -10.049 -10.049 dslf_fa13 1.250 -4.134 -5.168 omega 0.400 32.147 12.859 fa_dun 0.700 663.521 464.465 p_aa_pp 0.600 -69.949 -41.970 yhh_planarity 0.625 0.000 0.000 ref 1.000 170.937 170.937 rama_prepro 0.450 69.289 31.180 --------------------------------------------------- Total weighted score: -186.952 protocols.docking.DockingProtocol.metrics: unbound energy: -182.585 protocols.docking.DockingProtocol.metrics: bound energy: -186.952 protocols.docking.DockingProtocol.metrics: interaction energy: -4.36676 protocols.docking.DockingProtocol.metrics: rb_jump: 1 protocols.docking.DockingProtocol.metrics: unbound pose: protocols.docking.DockingProtocol.metrics: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.338 -1625.788 -549.516 fa_rep 0.186 635.971 118.087 fa_sol 0.242 858.723 207.811 fa_elec 0.026 -348.335 -9.057 fa_pair 0.164 -31.555 -5.175 hbond_sr_bb 0.245 -47.347 -11.600 hbond_lr_bb 0.245 -100.043 -24.511 hbond_bb_sc 0.245 -25.378 -6.218 hbond_sc 0.245 -8.347 -2.045 dslf_ss_dst 0.500 -15.294 -7.647 dslf_cs_ang 2.000 1.100 2.200 dslf_ss_dih 5.000 0.462 2.308 dslf_ca_dih 5.000 0.254 1.269 fa_dun 0.036 663.521 23.887 --------------------------------------------------- Total weighted score: -260.206 protocols.docking.DockingProtocol.metrics: bound pose: protocols.docking.DockingProtocol.metrics: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 0.338 -1645.760 -556.267 fa_rep 0.186 640.173 118.867 fa_sol 0.242 871.823 210.981 fa_elec 0.026 -348.063 -9.050 fa_pair 0.164 -33.488 -5.492 hbond_sr_bb 0.245 -47.347 -11.600 hbond_lr_bb 0.245 -100.043 -24.511 hbond_bb_sc 0.245 -25.864 -6.337 hbond_sc 0.245 -8.361 -2.048 dslf_ss_dst 0.500 -15.294 -7.647 dslf_cs_ang 2.000 1.100 2.200 dslf_ss_dih 5.000 0.462 2.308 dslf_ca_dih 5.000 0.254 1.269 fa_dun 0.036 663.521 23.887 --------------------------------------------------- Total weighted score: -263.439 protocols.docking.DockingProtocol.metrics: unbound energy: -260.206 protocols.docking.DockingProtocol.metrics: bound energy: -263.439 protocols.docking.DockingProtocol.metrics: interaction energy: -3.23264 protocols.docking.DockingProtocol.metrics: rb_jump: 1 core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/demo/D100_Docking.py:95: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.protocols.rigid import ( Finished D100_Docking in 0:00:47.540108

mac.clang.python310.PyRosetta.unit.D110_DNA_interface 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.10938 seconds. core.import_pose.import_pose: File '../test/data/dna_test.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name O5* to O5' core.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name C5* to C5' core.io.pose_from_sfr.PoseFromSFRBuilder: Number of nucleic acid residue fixups exceeds output limit. Rerun with -show_all_fixes to show everything. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: -12 C DG GUA:VirtualDNAPhosphate core.io.pose_from_sfr.PoseFromSFRBuilder: missing: P core.io.pose_from_sfr.PoseFromSFRBuilder: missing: O5' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C5' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C4' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C3' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: O3' core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 164 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 166 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 167 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 169 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 170 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 172 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 173 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 174 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:UpperRNA:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 175 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE:LowerDNA:VirtualDNAPhosphate core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 177 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 181 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 182 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 183 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 184 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 185 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 186 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT:UpperDNA core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for OP1 and OP2 for residue DT core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue DT core.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: N9 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N7 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C8 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: Connecting residues: 162 ( GUA:LowerDNA:VirtualDNAPhosphate ) and 163 ( CYT ) at atoms O3' and P core.conformation.Conformation: with mutual distances: 0.293633 and 0.00610344 core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 163 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 164 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 165 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 166 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 167 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 168 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 169 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 170 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 171 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 172 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 173 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 174 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 175 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 176 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 177 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 178 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 179 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 181 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 182 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 183 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 184 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 185 atom 2H2' (trying to store temperature in PDBInfo) core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 12 atom name N9 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.25456 seconds to load from binary core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.docking.DockMCMProtocol: in DockMCMProtocol.apply protocols.docking.DockMCMProtocol: Using the DockingTaskFactory. protocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockMCMCycle: /// Dockable Jumps: 1 /// protocols.docking.DockMCMCycle: /// Translation: 0.1 /// protocols.docking.DockMCMCycle: /// Rotation: 5 /// protocols.docking.DockMCMCycle: /// Scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.947733) (fa_rep 0.577238) (fa_sol 0.507356) (fa_elec 1) (pro_close 1) (hbond_sr_bb 2.80253) (hbond_lr_bb 2.80253) (hbond_bb_sc 2.80253) (hbond_sc 1.59624) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.68229) (p_aa_pp 0.612065) (ref 1) (res_type_constraint 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref -1.58548 -1.18225 3.39 1.61782 0.10405 -2.19778 0.838118 -1.81735 -1.53824 -1.26583 -1.40187 1.06144 -2.58097 -0.20752 9.93689 -2.59427 -1.18434 -1.42293 1.82099 0.209525 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: false protocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: p┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Working on decoy: dna_output_0.pdb rotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: false protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 388 rotamers at 34 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 406 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 406 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 406 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 406 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 406 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() Finished D110_DNA_interface in 0:00:41.036213

mac.clang.python310.PyRosetta.unit.D120_Ligand_interface 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 Finished D120_Ligand_interface in 0:00:16.238688

mac.clang.python310.PyRosetta.unit.T000_Imports 「click to collapse/expand」

vector1_int[1, 2, 3, 4] vector1_double[1, 2, 3, 4.5] vector1_std_string[a, b, c, d] std_set[1, 2, 3, 4] std_set[1, 2, 3, 4.5] std_set[a, b, c, d] Testing Python bindings for Rosetta... Init... ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=861559990 seed_offset=0 real_seed=861559990 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=861559990 RG_type=mt19937 Finished T000_Imports in 0:00:16.168424

mac.clang.python310.PyRosetta.unit.T005_Bindings 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Total residues: 0 Sequence: Fold tree: FOLD_TREE Total residues: 0 Sequence: Fold tree: FOLD_TREE ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: false EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: false HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: false HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionOP() PASSED ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: false EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: false HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: false HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP() PASSED ScoreFunction::show(): weights: energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: true EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: true HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: true HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP2() PASSED <pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x1031afc30> <pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x1031afc30> <pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x1031afc30> <pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x1031afc30> core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-492862494 seed_offset=0 real_seed=-492862494 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-492862494 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.974442 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T005_Bindings.py:48: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.protocols.toolbox.py_inheritance_test import * Finished T005_Bindings in 0:00:19.364618

mac.clang.python310.PyRosetta.unit.T006_Options 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git out:nstruct: 5 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -nstruct 5 -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 Finished T006_Options in 0:00:16.009679

mac.clang.python310.PyRosetta.unit.T007_TracerIO 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.02094 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB -------- Test/Demo for capturing Tracers output in PyRosetta -------- ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Captured IO: core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.02094 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git MyPyTracer.output_callback with argument: core.init: Checking for fconfig files in pwd and ./rosetta/flags MyPyTracer.output_callback with argument: MyPyTracer.output_callback with argument: core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 MyPyTracer.output_callback with argument: core.init: Rosetta extras: [] MyPyTracer.output_callback with argument: core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database MyPyTracer.output_callback with argument: basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1361329603 seed_offset=0 real_seed=1361329603 MyPyTracer.output_callback with argument: basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1361329603 RG_type=mt19937 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1361329603 seed_offset=0 real_seed=1361329603 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1361329603 RG_type=mt19937 /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T007_TracerIO.py:14: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. import rosetta, pyrosetta Finished T007_TracerIO in 0:00:17.263862

mac.clang.python310.PyRosetta.unit.T008_Serialization 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=146439262 seed_offset=0 real_seed=146439262 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=146439262 RG_type=mt19937 Finished T008_Serialization in 0:00:16.171045

mac.clang.python310.PyRosetta.unit.T009_Exceptions 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Exceptions type: <class 'RuntimeError'>, message: File: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rosetta_scripts/RosettaScriptsParser.cc:514 parser::protocol file must specify PROTOCOLS section core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1121791482 seed_offset=0 real_seed=-1121791482 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1121791482 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.03548 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 Finished T009_Exceptions in 0:00:20.208637

mac.clang.python310.PyRosetta.unit.T010_LoadPDB 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.05101 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.285255 seconds to load from binary core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.022659 seconds. basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth core.io.silent.SilentFileData: Reading all structures from ../test/data/test_in.silent core.io.silent.SilentFileData: Finished reading 8 structures from ../test/data/test_in.silent core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 Finished T010_LoadPDB in 0:00:19.928631

mac.clang.python310.PyRosetta.unit.T020_Pose_Bindings 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:26: DeprecationWarning: Pose.__len__ is deprecated, prefer 'pose.residues.__len__'. assert(len(pose1) == 8) # Deprecated /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:35: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for residue in pose1: # Deprecated /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:56: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'. assert(''.join([res.annotated_name() for res in pose1[1:9]]) == 'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]') # Deprecated /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:57: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'. assert(''.join([res.annotated_name() for res in pose1[-6:8]]) == 'DEFGH') # Deprecated Finished T020_Pose_Bindings in 0:00:17.396050

mac.clang.python310.PyRosetta.unit.T040_Types 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 Finished T040_Types in 0:00:16.168987

mac.clang.python310.PyRosetta.unit.T100_basic 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git General testing ---------------------------------------------- Creating Pose object... Pose from PDB... Building Pose from sequence... PDB file name: DSEEKFLR Total residues: 21 Sequence: DSEEKFLRRIGRFGYGYGPYE Fold tree: FOLD_TREE EDGE 1 21 -1 Dump PDB... accessing pose attributes PDB file name: ../test/data/test_in.pdb Total residues: 116 Sequence: DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL Fold tree: FOLD_TREE EDGE 1 116 -1 there are 116 residues in this pose object phi of residue 5 is -64.78549729348204 psi of residue 5 is -39.712439411727274 set phi of residue 5 to -60 set psi of residue 5 to -50 accessing residue 5 from pose Residue 5: ILE (ILE, I): Base: ILE Properties: POLYMER PROTEIN CANONICAL_AA HYDROPHOBIC ALIPHATIC BETA_BRANCHED_SIDECHAIN METALBINDING ALPHA_AA L_AA Variant types: Main-chain atoms: N CA C Backbone atoms: N CA C O H HA Side-chain atoms: CB CG1 CG2 CD1 HB 1HG1 2HG1 1HG2 2HG2 3HG2 1HD1 2HD1 3HD1 Atom Coordinates: N : -2.53898, 36.4415, 79.2297 CA : -1.97052, 36.1949, 80.5403 C : -2.23109, 37.3858, 81.4325 O : -2.50917, 37.2043, 82.6002 CB : -0.453211, 35.963, 80.4929 CG1: -0.175565, 34.5273, 80.077 CG2: 0.172042, 36.261, 81.8574 CD1: -0.927946, 33.5005, 80.9024 H : -1.93862, 36.5194, 78.4212 HA : -2.46732, 35.3543, 81.0219 HB : -0.0182833, 36.6096, 79.7313 1HG1: -0.458733, 34.4327, 79.0287 2HG1: 0.8975, 34.3623, 80.1785 1HG2: 1.24765, 36.092, 81.8094 2HG2: -0.0204952, 37.2987, 82.1272 3HG2: -0.264762, 35.6037, 82.6097 1HD1: -0.681316, 32.4982, 80.5509 2HD1: -0.643714, 33.5961, 81.9508 3HD1: -2.00002, 33.6654, 80.801 Mirrored relative to coordinates in ResidueType: FALSE accessing atoms from residue 5 -2.53898, 36.4415, 79.2297 xyz of at5N: -2.53898489237762 36.44151978598334 79.22969355726434 norm of xyz at5N: <bound method PyCapsule.norm of <pyrosetta.rosetta.numeric.xyzVector_double_t object at 0x10deb2a70>> vector1_core_conformation_Atom[-2.53898, 36.4415, 79.2297, -1.97052, 36.1949, 80.5403, -2.23109, 37.3858, 81.4325, -2.50917, 37.2043, 82.6002, -0.453211, 35.963, 80.4929, -0.175565, 34.5273, 80.077, 0.172042, 36.261, 81.8574, -0.927946, 33.5005, 80.9024, -1.93862, 36.5194, 78.4212, -2.46732, 35.3543, 81.0219, -0.0182833, 36.6096, 79.7313, -0.458733, 34.4327, 79.0287, 0.8975, 34.3623, 80.1785, 1.24765, 36.092, 81.8094, -0.0204952, 37.2987, 82.1272, -0.264762, 35.6037, 82.6097, -0.681316, 32.4982, 80.5509, -0.643714, 33.5961, 81.9508, -2.00002, 33.6654, 80.801] bond length of N-CA in residue 5 is 1.4496692726273892 bond angle of N-CA-C in residue 5 is 1.9094258533068345 setting bond length of N-CA in residue 5 to 1.5A setting bond angle of N-CA-C in residue 5 to 90 pose was generated from this pdb file: ../test/data/test_in.pdb pose numbering for chain A, residue 5, is 5 pdb chain letter and residue number for residue 5, is 5 A Residue 0: ALA (ALA, A): Base: ALA Properties: POLYMER PROTEIN CANONICAL_AA ALIPHATIC METALBINDING ALPHA_AA L_AA Variant types: Main-chain atoms: N CA C Backbone atoms: N CA C O H HA Side-chain atoms: CB 1HB 2HB 3HB Atom Coordinates: N : 0, 0, 0 CA : 1.458, 0, 0 C : 2.00885, 1.42017, 0 O : 1.38304, 2.33899, -0.528697 CB : 1.9878, -0.772763, -1.19909 H : -0.491969, 0.763905, -0.44104 HA : 1.79666, -0.489627, 0.91315 1HB : 3.07772, -0.76375, -1.18511 2HB : 1.63286, -1.80244, -1.15412 3HB : 1.63327, -0.30698, -2.11716 Mirrored relative to coordinates in ResidueType: FALSE core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.99567 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.022327 seconds. Finished T100_basic in 0:00:17.367896

mac.clang.python310.PyRosetta.unit.T110_numeric 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 Finished T110_numeric in 0:00:16.167955

mac.clang.python310.PyRosetta.unit.T120_core.RotamerSets 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-12516515 seed_offset=0 real_seed=-12516515 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-12516515 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.14304 seconds. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop Finished T120_core.RotamerSets in 0:00:05.385981

mac.clang.python310.PyRosetta.unit.T150_PyMOL_Integration 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.12589 seconds. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.256127 seconds to load from binary Finished T150_PyMOL_Integration in 0:00:06.129454

mac.clang.python310.PyRosetta.unit.T150_core.misc.lkball 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git 1 1 2 0 3 0 4 2 5 0 6 0 7 2 8 2 9 0 10 0 11 0 12 0 13 0 14 0 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1294291378 seed_offset=0 real_seed=-1294291378 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1294291378 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.10469 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.249673 seconds to load from binary Finished T150_core.misc.lkball in 0:00:06.093700

mac.clang.python310.PyRosetta.unit.T190_Bindings_Utility 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 Finished T190_Bindings_Utility in 0:00:02.447673

mac.clang.python310.PyRosetta.unit.T200_Scoring 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Scoring ---------------------------------------------- Creating standard fullatom score function and scoring Creating standard centroid score function and scoring Creating standard score function and scoring, again Creating standard score from scratch Adjusting weights and scoring weight for fa_atr set to: 1.0 ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 1) (fa_pair 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: true EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: true HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: true HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 Score break down for pose... all residue energies are None weighted energies for residue 5 None fa_atr: -0.593 fa_rep: 0.118 fa_pair: 0.000 fa_atr of residue 5 -0.5929040959214456 fa_atr for residue 5: -0.5929040959214456 manually calculating 2body context-independent energies between residues 4 and 5 fa_atr between 1 and 2: -0.42118788604496193 fa_pair between 1 and 2: 0.0 fa_rep between 1 and 2: 0.12092691972750393 ScoreType.fa_atrScoreType.fa_repScoreType.fa_solScoreType.fa_intra_atrScoreType.fa_intra_repScoreType.fa_intra_solScoreType.fa_intra_atr_xover4ScoreType.fa_intra_rep_xover4ScoreType.fa_intra_sol_xover4ScoreType.fa_intra_atr_nonproteinScoreType.fa_intra_rep_nonproteinScoreType.fa_intra_sol_nonproteinScoreType.fa_intra_RNA_base_phos_atrScoreType.fa_intra_RNA_base_phos_repScoreType.fa_intra_RNA_base_phos_solScoreType.fa_atr_dummyScoreType.fa_rep_dummyScoreType.fa_sol_dummyScoreType.fa_vdw_tinkerScoreType.lk_hackScoreType.lk_ballScoreType.lk_ball_wtdScoreType.lk_ball_isoScoreType.lk_ball_bridgeScoreType.lk_ball_bridge_uncplScoreType.lk_domeScoreType.lk_dome_isoScoreType.lk_dome_bridgeScoreType.lk_dome_bridge_uncplScoreType.lk_ball_bridge2ScoreType.lk_ball_bridge_uncpl2ScoreType.lk_dome_packScoreType.coarse_fa_atrScoreType.coarse_fa_repScoreType.coarse_fa_solScoreType.coarse_beadljScoreType.mm_lj_intra_repScoreType.mm_lj_intra_atrScoreType.mm_lj_inter_repScoreType.mm_lj_inter_atrScoreType.mm_twistScoreType.mm_bendScoreType.mm_stretchScoreType.lk_costhetaScoreType.lk_polarScoreType.lk_nonpolarScoreType.lk_polar_intra_RNAScoreType.lk_nonpolar_intra_RNAScoreType.fa_elecScoreType.fa_elec_bb_bbScoreType.fa_elec_bb_scScoreType.fa_elec_sc_scScoreType.fa_intra_elecScoreType.fa_imm_elecScoreType.h2o_hbondScoreType.dna_drScoreType.dna_bpScoreType.dna_bsScoreType.dna_refScoreType.peptide_bondScoreType.pcsScoreType.pcsTs1ScoreType.pcsTs2ScoreType.pcsTs3ScoreType.pcsTs4ScoreType.pcs2ScoreType.fastsaxsScoreType.saxs_scoreScoreType.saxs_cen_scoreScoreType.saxs_fa_scoreScoreType.pddf_scoreScoreType.fiberdiffractionScoreType.fiberdiffractiondensScoreType.epr_deer_scoreScoreType.fa_mbenvScoreType.fa_mbsolvScoreType.fa_elec_rna_phos_phosScoreType.fa_elec_rna_phos_sugrScoreType.fa_elec_rna_phos_baseScoreType.fa_elec_rna_sugr_sugrScoreType.fa_elec_rna_sugr_baseScoreType.fa_elec_rna_base_baseScoreType.fa_elec_rna_phos_phos_fastScoreType.fa_elec_rna_phos_sugr_fastScoreType.fa_elec_rna_phos_base_fastScoreType.fa_elec_rna_sugr_sugr_fastScoreType.fa_elec_rna_sugr_base_fastScoreType.fa_elec_rna_base_base_fastScoreType.fa_elec_aro_aroScoreType.fa_elec_aro_allScoreType.hack_aroScoreType.rna_fa_atr_baseScoreType.rna_fa_rep_baseScoreType.rna_data_backboneScoreType.ch_bondScoreType.ch_bond_bb_bbScoreType.ch_bond_sc_scScoreType.ch_bond_bb_scScoreType.pro_closeScoreType.rama2bScoreType.vdwScoreType.cenpackScoreType.cenpack_smoothScoreType.cen_hbScoreType.hybrid_vdwScoreType.gaussScoreType.rna_vdwScoreType.rnp_vdwScoreType.rna_base_backboneScoreType.rna_backbone_backboneScoreType.rna_repulsiveScoreType.rna_base_pair_pairwiseScoreType.rna_base_axis_pairwiseScoreType.rna_base_stagger_pairwiseScoreType.rna_base_stack_pairwiseScoreType.rna_base_stack_axis_pairwiseScoreType.rna_data_baseScoreType.rna_base_pairScoreType.rna_base_axisScoreType.rna_base_staggerScoreType.rna_base_stackScoreType.rna_base_stack_axisScoreType.rnp_base_pairScoreType.rnp_stackScoreType.rnp_stack_xyScoreType.rnp_pairScoreType.rnp_pair_distScoreType.rnp_aa_to_rna_backboneScoreType.rna_mg_pointScoreType.rna_mg_point_indirectScoreType.mgScoreType.mg_ligScoreType.mg_solScoreType.mg_refScoreType.hoh_refScoreType.rna_torsionScoreType.rna_torsion_scScoreType.rna_suiteScoreType.rna_jr_suiteScoreType.suiteness_bonusScoreType.tna_suiteScoreType.rna_sugar_closeScoreType.fa_stackScoreType.fa_stack_lowerScoreType.fa_stack_upperScoreType.fa_stack_aroScoreType.fa_stack_extScoreType.fa_stack_solScoreType.fa_stack_lrScoreType.fa_stack_rna_proteinScoreType.fa_stack_rna_protein_aroScoreType.ss_contact_worstScoreType.stack_elecScoreType.stack_elec_base_baseScoreType.stack_elec_base_bbScoreType.alignmentScoreType.dna_bb_torsionScoreType.dna_sugar_closeScoreType.dna_base_distanceScoreType.geom_sol_fastScoreType.geom_sol_fast_intra_RNAScoreType.fa_cust_pair_distScoreType.custom_atom_pairScoreType.orbitals_hpol_bbScoreType.pci_cation_piScoreType.pci_pi_piScoreType.pci_salt_bridgeScoreType.pci_hbondScoreType.arg_cation_piScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_lastScoreType.pythonScoreType.fa_pairScoreType.fa_pair_aro_aroScoreType.fa_pair_aro_polScoreType.fa_pair_pol_polScoreType.hbond_sr_bbScoreType.hbond_lr_bbScoreType.hbond_bb_scScoreType.hbond_sr_bb_scScoreType.hbond_lr_bb_scScoreType.hbond_scScoreType.hbond_intraScoreType.hbond_watScoreType.wat_entropyScoreType.hbondScoreType.npd_hbond_sr_bbScoreType.npd_hbond_lr_bbScoreType.npd_hbond_bb_scScoreType.npd_hbond_sr_bb_scScoreType.npd_hbond_lr_bb_scScoreType.npd_hbond_scScoreType.npd_hbond_intraScoreType.npd_hbondScoreType.fa_grpelecScoreType.PyRosettaTwoBodyContextDependentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextDependentEnergy_lastScoreType.interface_dd_pairScoreType.geom_solScoreType.geom_sol_intra_RNAScoreType.occ_sol_fittedScoreType.occ_sol_fitted_onebodyScoreType.occ_sol_exactScoreType.cen_rot_pairScoreType.cen_rot_pair_angScoreType.cen_rot_pair_dihScoreType.pairScoreType.cen_pair_smoothScoreType.MpairScoreType.MPPairScoreType.FaMPSolvScoreType.suckScoreType.rna_rgScoreType.rna_motifScoreType.facts_elecScoreType.facts_solvScoreType.facts_sasaScoreType.motif_dockScoreType.pointwaterScoreType.goapScoreType.goap_distScoreType.goap_angleScoreType.approximate_buried_unsat_penaltyScoreType.interchain_pairScoreType.interchain_vdwScoreType.gb_elecScoreType.multipole_elecScoreType.fa_sasaScoreType.dslf_ss_dstScoreType.dslf_cs_angScoreType.dslf_ss_dihScoreType.dslf_ca_dihScoreType.dslf_cbs_dsScoreType.dslf_fa13ScoreType.dslfc_cen_dstScoreType.dslfc_cb_dstScoreType.dslfc_angScoreType.dslfc_cb_dihScoreType.dslfc_bb_dihScoreType.dslfc_rotScoreType.dslfc_transScoreType.dslfc_RTScoreType.atom_pair_constraintScoreType.base_pair_constraintScoreType.coarse_chainbreak_constraintScoreType.constant_constraintScoreType.coordinate_constraintScoreType.angle_constraintScoreType.dihedral_constraintScoreType.big_bin_constraintScoreType.dunbrack_constraintScoreType.site_constraintScoreType.metalhash_constraintScoreType.metalbinding_constraintScoreType.rna_stub_coord_hackScoreType.bond_geometryScoreType.rna_bond_geometryScoreType.Hpol_bond_geometryScoreType.ramaScoreType.omegaScoreType.fa_dunScoreType.fa_dun_devScoreType.fa_dun_rotScoreType.fa_dun_semiScoreType.cen_rot_dunScoreType.dna_chiScoreType.p_aa_ppScoreType.p_aa_ssScoreType.yhh_planarityScoreType.hxl_torsScoreType.h2o_intraScoreType.refScoreType.ref_ncScoreType.seqdep_refScoreType.nmer_refScoreType.nmer_pssmScoreType.nmer_svmScoreType.envsmoothScoreType.e_pHScoreType.rna_bulgeScoreType.dna_dihedral_bbScoreType.dna_dihedral_chiScoreType.dna_dihedral_sugarScoreType.sugar_bbScoreType.free_suiteScoreType.free_2HOprimeScoreType.free_side_chainScoreType.free_baseScoreType.free_resScoreType.free_dofScoreType.intermolScoreType.other_poseScoreType.special_rotScoreType.PB_elecScoreType.cen_env_smoothScoreType.cbeta_smoothScoreType.cen_rot_envScoreType.cen_rot_cbetaScoreType.envScoreType.cbetaScoreType.DFIREScoreType.MenvScoreType.McbetaScoreType.Menv_non_helixScoreType.Menv_terminiScoreType.Menv_tm_projScoreType.MlipoScoreType.rgScoreType.rg_localScoreType.coScoreType.hs_pairScoreType.ss_pairScoreType.rsigmaScoreType.sheetScoreType.burial_v2ScoreType.burialScoreType.abegoScoreType.covalent_labelingScoreType.covalent_labeling_faScoreType.hrf_ms_labelingScoreType.hrf_dynamicsScoreType.ccs_immsScoreType.depc_msScoreType.rnp_envScoreType.loop_closeScoreType.missing_resScoreType.MPEnvScoreType.MPCbetaScoreType.MPLipoScoreType.MPTerminiScoreType.MPNonHelixScoreType.MPTMProjScoreType.FaMPEnvScoreType.FaMPEnvSmoothScoreType.fa_water_to_bilayerScoreType.f_elec_lipidlayerScoreType.FaMPAsymEzCBScoreType.FaMPAsymEzCGScoreType.MPResidueLipophilicityScoreType.span_insScoreType.mp_span_angScoreType.MPHelicalityScoreType.natbias_ssScoreType.natbias_hsScoreType.natbias_hhScoreType.natbias_stwistScoreType.aa_cmpScoreType.dock_ens_confScoreType.csaScoreType.dcScoreType.rdcScoreType.rdc_segmentsScoreType.rdc_rohlScoreType.nmr_pcsScoreType.nmr_rdcScoreType.nmr_preScoreType.cen_pair_motifsScoreType.cen_pair_motif_degreeScoreType.holesScoreType.holes_decoyScoreType.holes_reslScoreType.holes_minScoreType.holes_min_meanScoreType.rna_chem_shiftScoreType.rna_chem_mapScoreType.rna_chem_map_loresScoreType.rna_partitionScoreType.dab_sasaScoreType.dab_sevScoreType.saScoreType.d2h_saScoreType.ProQMScoreType.ProQScoreType.interchain_envScoreType.interchain_contactScoreType.chainbreakScoreType.linear_chainbreakScoreType.overlap_chainbreakScoreType.distance_chainbreakScoreType.dof_constraintScoreType.branch_connScoreType.linear_branch_connScoreType.rama_preproScoreType.paa_abego3ScoreType.cart_bondedScoreType.cart_bonded_angleScoreType.cart_bonded_lengthScoreType.cart_bonded_ringScoreType.cart_bonded_torsionScoreType.cart_bonded_properScoreType.cart_bonded_improperScoreType.gen_bondedScoreType.gen_bonded_bondScoreType.gen_bonded_angleScoreType.gen_bonded_torsionScoreType.gen_bonded_improperScoreType.neigh_vectScoreType.neigh_countScoreType.neigh_vect_rawScoreType.symE_bonusScoreType.sym_ligScoreType.mhc_epitopeScoreType.pack_statScoreType.rmsScoreType.res_type_constraintScoreType.res_type_linking_constraintScoreType.pocket_constraintScoreType.backbone_stub_constraintScoreType.backbone_stub_linear_constraintScoreType.surfaceScoreType.p_aaScoreType.unfoldedScoreType.split_unfolded_two_bodyScoreType.fa_atr_refScoreType.fa_rep_refScoreType.fa_sol_refScoreType.fa_elec_refScoreType.hbond_refScoreType.dslf_fa13_refScoreType.fa_intra_atr_refScoreType.fa_intra_rep_refScoreType.fa_intra_sol_refScoreType.pro_close_refScoreType.fa_dun_refScoreType.fa_dun_dev_refScoreType.fa_dun_rot_refScoreType.fa_dun_semi_refScoreType.rama_refScoreType.p_aa_pp_refScoreType.omega_refScoreType.mm_lj_intra_rep_refScoreType.mm_lj_intra_atr_refScoreType.mm_twist_refScoreType.elec_dens_fastScoreType.elec_dens_windowScoreType.elec_dens_whole_structure_caScoreType.elec_dens_whole_structure_allatomScoreType.elec_dens_atomwiseScoreType.grid_vdwScoreType.xtal_mlScoreType.xtal_rworkScoreType.xtal_rfreeScoreType.hpatchScoreType.Menv_smoothScoreType.wat_desolvScoreType.ring_closeScoreType.aa_repeatScoreType.aa_compositionScoreType.aspartimide_penaltyScoreType.hbnetScoreType.buried_unsatisfied_penaltyScoreType.netchargeScoreType.voids_penaltyScoreType.sap_constraintScoreType.dna_envScoreType.dna_pairScoreType.dump_trajectoryScoreType.PyRosettaEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaEnergy_lastScoreType.sidechain_neighborsScoreType.target_clashScoreType.membrane_span_constraintScoreType.membrane_span_term_z_constraintScoreType.aromatic_restraintScoreType.rna_coarse_distScoreType.total_scoreScoreType.dummy_score_type identifying hydrogen bonds in structure core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.11472 seconds. core.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.248058 seconds to load from binary basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine core.scoring.ScoreFunction: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -5.202 -5.202 fa_rep 1.000 1.049 1.049 fa_pair 1.000 0.000 0.000 --------------------------------------------------- Total weighted score: -4.153 core.scoring.Energies: E fa_atr fa_rep fa_pair core.scoring.Energies: E(i) 1 -0.30 0.06 0.00 core.scoring.Energies: E(i) 2 -0.51 0.12 0.00 core.scoring.Energies: E(i) 3 -0.60 0.11 0.00 core.scoring.Energies: E(i) 4 -0.59 0.12 0.00 core.scoring.Energies: E(i) 5 -0.59 0.12 0.00 core.scoring.Energies: E(i) 6 -0.60 0.11 0.00 core.scoring.Energies: E(i) 7 -0.60 0.11 0.00 core.scoring.Energies: E(i) 8 -0.59 0.12 0.00 core.scoring.Energies: E(i) 9 -0.52 0.12 0.00 core.scoring.Energies: E(i) 10 -0.31 0.06 0.00 core.scoring.Energies: total_energy fa_atr -5.202 core.scoring.Energies: total_energy fa_rep 1.049 core.scoring.Energies: total_energy fa_pair 0.000 core.scoring.Energies: E fa_atr fa_rep fa_pair core.scoring.Energies: E(i) 5 -0.59 0.12 0.00 core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy core.scoring.hbonds.HBondSet: #A 6 HIS N A 2 ALA O 2.04 144.3 129.5 -90.7 1.000 -0.591 core.scoring.hbonds.HBondSet: #A 8 ILE N A 4 THR O 2.02 165.0 165.8 -132.1 1.000 -1.102 core.scoring.hbonds.HBondSet: #A 9 LEU N A 5 ILE O 2.26 163.0 149.7 -108.0 1.000 -0.865 core.scoring.hbonds.HBondSet: #A 10 ASP N A 7 SER O 1.99 118.8 121.9 -72.7 1.000 -0.053 core.scoring.hbonds.HBondSet: #A 11 TRP N A 7 SER O 2.13 163.6 152.7 150.3 1.000 -1.338 core.scoring.hbonds.HBondSet: #A 12 ILE N A 8 ILE O 2.03 139.2 140.6 -123.7 1.000 -0.721 core.scoring.hbonds.HBondSet: #A 13 GLU N A 9 LEU O 2.04 165.1 162.3 -156.5 1.000 -1.224 core.scoring.hbonds.HBondSet: #A 14 ASP N A 10 ASP O 1.86 150.2 152.5 -107.8 1.000 -0.689 core.scoring.hbonds.HBondSet: #A 15 ASN ND2A 11 TRP O 1.74 167.5 145.0 55.4 0.576 -1.075 core.scoring.hbonds.HBondSet: #A 15 ASN N A 12 ILE O 1.90 129.6 117.0 -123.3 1.000 -0.502 core.scoring.hbonds.HBondSet: #A 16 LEU N A 12 ILE O 2.12 139.7 156.3 41.7 1.000 -0.648 core.scoring.hbonds.HBondSet: #A 51 TYR OH A 13 GLU OE1 2.33 127.5 132.6 175.2 0.694 -0.057 core.scoring.hbonds.HBondSet: #A 55 ARG NH1A 13 GLU OE2 1.34 170.5 131.0 -58.3 0.812 -0.243 core.scoring.hbonds.HBondSet: #A 18 SER N A 15 ASN O 2.25 125.4 126.6 135.8 1.000 -0.507 core.scoring.hbonds.HBondSet: #A 56 LYS NZ A 19 PRO O 2.09 136.2 127.1 -155.2 0.835 -0.338 core.scoring.hbonds.HBondSet: #A 26 SER N A 22 LEU O 1.89 153.1 161.7 -159.5 1.000 -0.965 core.scoring.hbonds.HBondSet: #A 27 GLU N A 23 GLU O 1.90 127.2 124.4 -127.4 1.000 -0.529 core.scoring.hbonds.HBondSet: #A 28 ARG N A 24 LYS O 2.13 151.6 161.0 139.1 1.000 -0.876 core.scoring.hbonds.HBondSet: #A 30 GLY N A 28 ARG O 2.49 110.6 116.7 -151.7 1.000 -0.033 core.scoring.hbonds.HBondSet: #A 35 HIS N A 32 SER OG 2.29 149.9 129.3 42.4 0.412 -1.133 core.scoring.hbonds.HBondSet: #A 36 LEU N A 32 SER O 2.00 150.7 167.4 51.1 1.000 -0.802 core.scoring.hbonds.HBondSet: #A 37 GLN N A 33 LYS O 2.10 152.4 144.0 -111.3 1.000 -0.862 core.scoring.hbonds.HBondSet: #A 38 ARG N A 34 TRP O 2.05 155.6 134.2 -129.9 1.000 -1.268 core.scoring.hbonds.HBondSet: #A 39 MET N A 35 HIS O 1.83 162.3 167.2 121.8 1.000 -0.888 core.scoring.hbonds.HBondSet: #A 40 PHE N A 36 LEU O 2.00 162.8 150.8 -90.5 1.000 -1.000 core.scoring.hbonds.HBondSet: #A 41 LYS N A 37 GLN O 1.92 156.7 151.5 -106.1 1.000 -0.897 core.scoring.hbonds.HBondSet: #A 42 LYS N A 38 ARG O 2.04 174.7 160.8 -124.7 1.000 -1.211 core.scoring.hbonds.HBondSet: #A 43 GLU N A 39 MET O 1.81 133.8 142.7 -148.9 1.000 -0.720 core.scoring.hbonds.HBondSet: #A 44 THR N A 40 PHE O 1.84 148.2 139.0 -104.0 1.000 -0.626 core.scoring.hbonds.HBondSet: #A 46 HIS N A 44 THR OG1 2.38 140.9 115.1 31.0 0.647 -0.563 core.scoring.hbonds.HBondSet: #A 51 TYR N A 47 SER O 2.31 143.2 157.6 -134.7 1.000 -0.475 core.scoring.hbonds.HBondSet: #A 52 ILE N A 48 LEU O 2.04 169.5 172.7 -140.4 1.000 -1.110 core.scoring.hbonds.HBondSet: #A 53 ARG N A 49 GLY O 2.27 160.5 141.5 -138.6 1.000 -1.219 core.scoring.hbonds.HBondSet: #A 54 SER N A 50 GLN O 2.03 139.9 119.8 -107.0 1.000 -0.580 core.scoring.hbonds.HBondSet: #A 55 ARG N A 51 TYR O 1.91 145.7 149.7 -119.9 1.000 -0.733 core.scoring.hbonds.HBondSet: #A 56 LYS N A 52 ILE O 2.05 152.8 145.5 -144.7 1.000 -1.268 core.scoring.hbonds.HBondSet: #A 57 MET N A 53 ARG O 1.90 161.7 154.0 -106.5 1.000 -0.970 core.scoring.hbonds.HBondSet: #A 58 THR N A 54 SER O 2.05 153.5 133.7 -110.9 1.000 -0.941 core.scoring.hbonds.HBondSet: #A 59 GLU N A 55 ARG O 2.06 152.9 137.4 -113.4 1.000 -0.939 core.scoring.hbonds.HBondSet: #A 55 ARG NE A 113 LEU O 2.13 147.9 119.9 -95.9 0.859 -0.450 core.scoring.hbonds.HBondSet: #A 55 ARG NH2A 113 LEU O 1.82 143.4 172.4 178.3 0.859 -0.454 core.scoring.hbonds.HBondSet: #A 60 ILE N A 56 LYS O 1.92 158.0 145.1 -109.1 1.000 -0.960 core.scoring.hbonds.HBondSet: #A 56 LYS NZ A 78 TYR O 1.99 147.6 161.9 -149.3 0.976 -0.347 core.scoring.hbonds.HBondSet: #A 61 ALA N A 57 MET O 2.19 141.3 144.0 -107.9 1.000 -0.481 core.scoring.hbonds.HBondSet: #A 62 GLN N A 58 THR O 2.32 147.4 145.9 -134.5 1.000 -0.741 core.scoring.hbonds.HBondSet: #A 63 LYS N A 59 GLU O 2.38 148.8 139.1 -123.6 1.000 -0.599 core.scoring.hbonds.HBondSet: #A 78 TYR OH A 59 GLU OE1 2.33 163.0 127.0 55.3 0.882 -0.201 core.scoring.hbonds.HBondSet: #A 64 LEU N A 60 ILE O 2.21 144.1 134.6 -117.2 1.000 -0.669 core.scoring.hbonds.HBondSet: #A 66 GLU N A 62 GLN O 2.15 126.2 128.1 -135.5 1.000 -0.625 core.scoring.hbonds.HBondSet: #A 102 ARG NH1A 64 LEU O 2.20 150.3 103.2 -43.0 0.859 -0.641 core.scoring.hbonds.HBondSet: #A 69 GLU N A 67 SER OG 1.98 163.8 131.5 73.0 0.459 -2.039 core.scoring.hbonds.HBondSet: #A 77 ARG NH2A 69 GLU OE1 2.08 111.0 127.8 164.8 0.600 -0.556 core.scoring.hbonds.HBondSet: #A 102 ARG NH2A 69 GLU O 1.73 172.3 129.2 104.5 0.647 -0.841 core.scoring.hbonds.HBondSet: #A 74 LEU N A 70 PRO O 2.10 138.8 143.2 -162.9 1.000 -1.132 core.scoring.hbonds.HBondSet: #A 75 ALA N A 71 ILE O 1.85 153.0 140.3 -108.4 1.000 -0.788 core.scoring.hbonds.HBondSet: #A 76 GLU N A 72 LEU O 2.12 179.0 157.2 -97.9 1.000 -1.108 core.scoring.hbonds.HBondSet: #A 77 ARG N A 73 TYR O 2.25 145.4 127.3 -111.3 1.000 -0.591 core.scoring.hbonds.HBondSet: #A 78 TYR N A 74 LEU O 2.27 139.7 142.0 -109.7 1.000 -0.357 core.scoring.hbonds.HBondSet: #A 80 PHE N A 75 ALA O 1.93 151.5 158.1 109.3 1.000 -0.785 core.scoring.hbonds.HBondSet: #A 85 THR N A 82 SER OG 2.28 168.9 144.9 9.5 0.482 -0.986 core.scoring.hbonds.HBondSet: #A 86 LEU N A 82 SER O 2.39 154.0 131.8 -121.2 1.000 -0.707 core.scoring.hbonds.HBondSet: #A 87 THR N A 83 GLN O 1.58 162.4 157.0 -131.4 1.000 -0.163 core.scoring.hbonds.HBondSet: #A 88 ARG N A 84 GLN O 1.93 164.6 148.5 -104.7 1.000 -1.041 core.scoring.hbonds.HBondSet: #A 89 THR N A 85 THR O 2.15 160.7 139.8 -119.7 1.000 -1.116 core.scoring.hbonds.HBondSet: #A 90 PHE N A 86 LEU O 1.84 164.3 149.9 -87.9 1.000 -0.895 core.scoring.hbonds.HBondSet: #A 91 LYS N A 87 THR O 2.05 156.2 143.4 -111.4 1.000 -0.976 core.scoring.hbonds.HBondSet: #A 92 ASN N A 88 ARG O 2.11 145.3 137.3 -113.7 1.000 -0.732 core.scoring.hbonds.HBondSet: #A 93 TYR N A 89 THR O 2.20 132.5 141.4 -131.1 1.000 -0.528 core.scoring.hbonds.HBondSet: #A 93 TYR N A 90 PHE O 2.17 133.3 101.2 -94.2 1.000 -0.015 core.scoring.hbonds.HBondSet: #A 94 PHE N A 90 PHE O 1.91 148.0 158.2 -147.9 1.000 -0.887 core.scoring.hbonds.HBondSet: #A 95 ASP N A 91 LYS O 1.86 129.3 118.4 -77.4 1.000 -0.164 core.scoring.hbonds.HBondSet: #A 93 TYR OH A 111 ARG O 1.83 153.2 166.2 98.5 0.624 -0.510 core.scoring.hbonds.HBondSet: #A 111 ARG NH1A 93 TYR O 2.39 132.6 132.2 -117.9 0.624 -0.001 core.scoring.hbonds.HBondSet: #A 111 ARG NH1A 95 ASP OD2 1.88 140.2 140.4 -85.8 0.435 -0.369 core.scoring.hbonds.HBondSet: #A 111 ARG NH2A 95 ASP OD2 1.97 137.7 130.0 27.8 0.435 -1.037 core.scoring.hbonds.HBondSet: #A 101 TYR N A 97 PRO O 2.06 151.2 145.9 -135.7 1.000 -1.111 core.scoring.hbonds.HBondSet: #A 102 ARG N A 98 PRO O 2.03 134.2 138.7 -133.9 1.000 -0.762 core.scoring.hbonds.HBondSet: #A 103 MET N A 99 HIS O 2.13 143.0 152.2 -153.1 1.000 -0.914 core.scoring.hbonds.HBondSet: #A 112 PHE N A 109 GLU O 2.04 153.8 151.0 -144.0 1.000 -1.177 core.scoring.hbonds.HBondSet: #A 114 HIS NE2A 109 GLU OE2 2.35 163.9 126.7 64.4 0.388 -0.463 core.scoring.hbonds.HBondSet: #A 116 LEU N A 114 HIS O 1.65 145.1 121.9 -164.6 1.000 -1.004 Finished T200_Scoring in 0:00:06.666680

mac.clang.python310.PyRosetta.unit.T201_Scoring_pre_talaris 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -restore_pre_talaris_2013_behavior -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-40681057 seed_offset=0 real_seed=-40681057 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-40681057 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 74 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.058638 seconds. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack library took 0.067042 seconds to load from binary Finished T201_Scoring_pre_talaris in 0:00:05.172056

mac.clang.python310.PyRosetta.unit.T220_AtomAtomPairEnergies 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.98315 seconds. core.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34 core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162 core.conformation.Conformation: [ WARNING ] miss┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Printing individual energies: res-res atr score emap: -2.5584311767440906 res-res atr score pairwise: -2.5584311767440906 res-res rep score emap: 3.515015877828057 res-res rep score pairwise: 3.515015877828057 res-res solv score emap: 0.7697815585356838 res-res solv score pairwise: 0.7697815585356838 Checking if scores match... Score did match, yay... ing heavyatom: CD on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1 core.conformation.Conformation: Found disulfide between residues 1 119 core.conformation.Conformation: Found disulfide between residues 40 56 core.conformation.Conformation: Found disulfide between residues 133 194 core.conformation.Conformation: Found disulfide between residues 161 175 core.conformation.Conformation: Found disulfide between residues 184 213 core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.240181 seconds to load from binary core.pack.pack_rotamers: built 238 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph Finished T220_AtomAtomPairEnergies in 0:00:06.750641

mac.clang.python310.PyRosetta.unit.T250_Constraints 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git constraints ---------------------------------------------- Score before constraints applied: 949.3120641217009 Score after constraints applied: 1195.8122748998228 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.14181 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.234482 seconds to load from binary Finished T250_Constraints in 0:00:06.289378

mac.clang.python310.PyRosetta.unit.T300_PyJobDistributor 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Working on decoy: _jd_test_4.pdb Working on decoy: _jd_test_3.pdb Working on decoy: _jd_test_9.pdb Working on decoy: _jd_test_8.pdb Working on decoy: _jd_test_7.pdb Working on decoy: _jd_test_0.pdb Working on decoy: _jd_test_1.pdb Working on decoy: _jd_test_2.pdb Working on decoy: _jd_test_5.pdb Working on decoy: _jd_test_6.pdb Working on decoy: _jd_at_test_7.pdb.gz Working on decoy: _jd_at_test_1.pdb.gz Working on decoy: _jd_at_test_0.pdb.gz Working on decoy: _jd_at_test_2.pdb.gz Working on decoy: _jd_at_test_4.pdb.gz Working on decoy: _jd_at_test_8.pdb.gz Working on decoy: _jd_at_test_3.pdb.gz Working on decoy: _jd_at_test_9.pdb.gz Working on decoy: _jd_at_test_5.pdb.gz Working on decoy: _jd_at_test_6.pdb.gz core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.04654 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.239365 seconds to load from binary Finished T300_PyJobDistributor in 0:00:06.373430

mac.clang.python310.PyRosetta.unit.T400_Refinement 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.980809 seconds. core.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10 core.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10 resnum BB CHI NU BRANCH 001 TRUE FALSE FALSE FALSE 002 TRUE FALSE FALSE FALSE 003 TRUE FALSE FALSE FALSE 004 TRUE FALSE FALSE FALSE 005 TRUE FALSE FALSE FALSE 006 TRUE FALSE FALSE FALSE 007 TRUE FALSE FALSE FALSE 008 TRUE FALSE FALSE FALSE 009 TRUE FALSE FALSE FALSE 010 FALSE FALSE FALSE FALSE ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Refinement ---------------------------------------------- setting up a move map setting all backbone movement to true, and residue 10 to false outputting movemap mover: ClassicFragmentMover, 3mer Creating standard score function with patch and scoring mover: SmallMover Mover name: Small, Mover type: SmallMover, Mover current tag:NoTag Max angle for helices (H): 0 Max angle for strands (E): 5 Max angle for loops (L): 50 Temperature factor (kT): 0.5 Number of moves: 1 mover: ShearMover Mover name: Shear, Mover type: ShearMover, Mover current tag:NoTag Max angle for helices (H): 0 Max angle for strands (E): 50 Max angle for loops (L): 6 Temperature factor (kT): 0.5 Number of moves: 1 mover: MinMover mover: MonteCarlo protocols.moves.MonteCarlo: "Temperature" (kT): 1 Total Trials: 4 Lowest Score: 23.6488 Last Accepted Score: 23.6488 last_accept = 23.6488 mover: SequenceMover mover: TrialMover core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.230331 seconds to load from binary core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 23.6488 23.6488 protocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820 protocols.moves.MonteCarlo: MC: 1 23.6488 23.6488 23.6488 23.6488 0 0 0 accepted score beat low protocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820 basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth core.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt core.scoring.AtomVDW: Openning alternative vdw file: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/chemical/atom_type_sets/centroid_rot//min.txt core.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN protocols.TrialMover: Acceptance rate: 1 protocols.moves.MonteCarlo: MC: 1 22.6785 22.6785 22.6785 22.6785 0 0 0 accepted score beat low protocols.moves.TrialCounter: ClassicFragmentM trials= 1; accepts= 1.0000; energy_drop/trial= -0.97029 protocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820 Finished T400_Refinement in 0:00:07.923597

mac.clang.python310.PyRosetta.unit.T500_Packing 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Packing and Design ---------------------------------------------- mover: PackRotamersMover #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 TRUE FALSE ASP:NtermProteinFull 2 TRUE FALSE ALA 3 TRUE FALSE ILE 4 TRUE FALSE THR 5 FALSE FALSE 6 TRUE FALSE HIS,HIS_D 7 TRUE FALSE SER 8 TRUE FALSE ILE 9 TRUE FALSE LEU 10 TRUE FALSE ASP 11 TRUE FALSE TRP 12 TRUE FALSE ILE 13 TRUE FALSE GLU 14 TRUE FALSE ASP 15 TRUE FALSE ASN 16 TRUE FALSE LEU 17 TRUE FALSE GLU 18 TRUE FALSE SER 19 TRUE FALSE PRO 20 TRUE FALSE LEU 21 TRUE FALSE SER 22 TRUE FALSE LEU 23 TRUE FALSE GLU 24 TRUE FALSE LYS 25 TRUE FALSE VAL 26 TRUE FALSE SER 27 TRUE FALSE GLU 28 TRUE FALSE ARG 29 TRUE FALSE SER 30 TRUE FALSE GLY 31 TRUE FALSE TYR 32 TRUE FALSE SER 33 TRUE FALSE LYS 34 TRUE FALSE TRP 35 TRUE FALSE HIS,HIS_D 36 TRUE FALSE LEU 37 TRUE FALSE GLN 38 TRUE FALSE ARG 39 TRUE FALSE MET 40 TRUE FALSE PHE 41 TRUE FALSE LYS 42 TRUE FALSE LYS 43 TRUE FALSE GLU 44 TRUE FALSE THR 45 TRUE FALSE GLY 46 TRUE FALSE HIS,HIS_D 47 TRUE FALSE SER 48 TRUE FALSE LEU 49 TRUE FALSE GLY 50 TRUE FALSE GLN 51 TRUE FALSE TYR 52 TRUE FALSE ILE 53 TRUE FALSE ARG 54 TRUE FALSE SER 55 TRUE FALSE ARG 56 TRUE FALSE LYS 57 TRUE FALSE MET 58 TRUE FALSE THR 59 TRUE FALSE GLU 60 TRUE FALSE ILE 61 TRUE FALSE ALA 62 TRUE FALSE GLN 63 TRUE FALSE LYS 64 TRUE FALSE LEU 65 TRUE FALSE LYS 66 TRUE FALSE GLU 67 TRUE FALSE SER 68 TRUE FALSE ASN 69 TRUE FALSE GLU 70 TRUE FALSE PRO 71 TRUE FALSE ILE 72 TRUE FALSE LEU 73 TRUE FALSE TYR 74 TRUE FALSE LEU 75 TRUE FALSE ALA 76 TRUE FALSE GLU 77 TRUE FALSE ARG 78 TRUE FALSE TYR 79 TRUE FALSE GLY 80 TRUE FALSE PHE 81 TRUE FALSE GLU 82 TRUE FALSE SER 83 TRUE FALSE GLN 84 TRUE FALSE GLN 85 TRUE FALSE THR 86 TRUE FALSE LEU 87 TRUE FALSE THR 88 TRUE FALSE ARG 89 TRUE FALSE THR 90 TRUE FALSE PHE 91 TRUE FALSE LYS 92 TRUE FALSE ASN 93 TRUE FALSE TYR 94 TRUE FALSE PHE 95 TRUE FALSE ASP 96 TRUE FALSE VAL 97 TRUE FALSE PRO 98 TRUE FALSE PRO 99 TRUE FALSE HIS,HIS_D 100 TRUE FALSE LYS 101 TRUE FALSE TYR 102 TRUE FALSE ARG 103 TRUE FALSE MET 104 TRUE FALSE THR 105 TRUE FALSE ASN 106 TRUE FALSE MET 107 TRUE FALSE GLN 108 TRUE FALSE GLY 109 TRUE FALSE GLU 110 TRUE FALSE SER 111 TRUE FALSE ARG 112 TRUE FALSE PHE 113 TRUE FALSE LEU 114 TRUE FALSE HIS,HIS_D 115 TRUE FALSE PRO 116 TRUE FALSE LEU:CtermProteinFull Mover name: PackRotamersMover, Mover type: PackRotamersMover, Mover current tag:NoTag Score function: ref2015 #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 TRUE TRUE ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull 2 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 3 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 4 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 5 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 6 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 7 FALSE FALSE 8 FALSE FALSE 9 FALSE FALSE 10 FALSE FALSE 11 FALSE FALSE 12 FALSE FALSE 13 FALSE FALSE 14 FALSE FALSE 15 FALSE FALSE 16 FALSE FALSE 17 FALSE FALSE 18 FALSE FALSE 19 FALSE FALSE 20 FALSE FALSE 21 FALSE FALSE 22 FALSE FALSE 23 FALSE FALSE 24 FALSE FALSE 25 FALSE FALSE 26 FALSE FALSE 27 FALSE FALSE 28 FALSE FALSE 29 FALSE FALSE 30 FALSE FALSE 31 FALSE FALSE 32 FALSE FALSE 33 FALSE FALSE 34 FALSE FALSE 35 FALSE FALSE 36 FALSE FALSE 37 FALSE FALSE 38 FALSE FALSE 39 FALSE FALSE 40 FALSE FALSE 41 FALSE FALSE 42 FALSE FALSE 43 FALSE FALSE 44 FALSE FALSE 45 FALSE FALSE 46 FALSE FALSE 47 FALSE FALSE 48 FALSE FALSE 49 FALSE FALSE 50 FALSE FALSE 51 FALSE FALSE 52 FALSE FALSE 53 FALSE FALSE 54 FALSE FALSE 55 FALSE FALSE 56 FALSE FALSE 57 FALSE FALSE 58 FALSE FALSE 59 FALSE FALSE 60 FALSE FALSE 61 FALSE FALSE 62 FALSE FALSE 63 FALSE FALSE 64 FALSE FALSE 65 FALSE FALSE 66 FALSE FALSE 67 FALSE FALSE 68 FALSE FALSE 69 FALSE FALSE 70 FALSE FALSE 71 FALSE FALSE 72 FALSE FALSE 73 FALSE FALSE 74 FALSE FALSE 75 FALSE FALSE 76 FALSE FALSE 77 FALSE FALSE 78 FALSE FALSE 79 FALSE FALSE 80 FALSE FALSE 81 FALSE FALSE 82 FALSE FALSE 83 FALSE FALSE 84 FALSE FALSE 85 FALSE FALSE 86 FALSE FALSE 87 FALSE FALSE 88 FALSE FALSE 89 FALSE FALSE 90 FALSE FALSE 91 FALSE FALSE 92 FALSE FALSE 93 FALSE FALSE 94 FALSE FALSE 95 FALSE FALSE 96 FALSE FALSE 97 FALSE FALSE 98 FALSE FALSE 99 FALSE FALSE 100 FALSE FALSE 101 FALSE FALSE 102 FALSE FALSE 103 FALSE FALSE 104 FALSE FALSE 105 FALSE FALSE 106 FALSE FALSE 107 FALSE FALSE 108 FALSE FALSE 109 FALSE FALSE 110 FALSE FALSE 111 FALSE FALSE 112 FALSE FALSE 113 FALSE FALSE 114 FALSE FALSE 115 FALSE FALSE 116 FALSE FALSE GGGG core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.15048 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.pack.task: Packer task: initialize from command line() basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.245669 seconds to load from binary core.pack.pack_rotamers: built 2848 rotamers at 115 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1023 rotamers at 6 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2822 rotamers at 115 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.minimization_packing.PackRotamersMover: [ WARNING ] undefined ScoreFunction -- creating a default one core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.pack_rotamers: built 4 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph Finished T500_Packing in 0:00:12.203178

mac.clang.python310.PyRosetta.unit.T600_Docking 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.00117 seconds. core.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34 core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1 core.conformation.Conformation: Found disulfide between residues 1 119 core.conformation.Conformation: Found disulfide between residues 40 56 core.conformation.Conformation: Found disulfide between residues 133 194 core.conformation.Conformation: Found disulfide between residues 161 175 core.conformation.Conformation: Found disulfide between residues 184 213 core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.240812 seconds to load from binary core.pack.pack_rotamers: built 238 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.025153 seconds. protocols.moves.RigidBodyMover: Spin: Jump (before): RT -0.389931 0.810342 -0.437379 -0.892411 -0.449663 -0.0375013 -0.227062 0.375699 0.898495 -12.6138 -39.3747 8.5794 protocols.moves.RigidBodyMover: Spin: Rot (before): 40.7713 27.6633 9.48574 protocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.106732 -0.00891842 -0.994248 -0.993895 0.0271569 -0.106937 0.0279544 0.999591 -0.00596546 -11.6523 -39.1223 10.5884 protocols.moves.RigidBodyMover: Spin: Rot (after): 40.7713 27.6633 9.48574 protocols.moves.RigidBodyMover: Spin: --- basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt protocols.docking.DockingInitialPerturbation: sliding into contact protocols.docking.DockingInitialPerturbation: Moving away protocols.docking.DockingInitialPerturbation: Moving together protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.36 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Acceptance rate is: 0.16 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.2 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.22 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.22 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.12 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.Doc┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Docking ---------------------------------------------------- kingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.24 Finished T600_Docking in 0:00:10.154493

mac.clang.python310.PyRosetta.unit.T650_LoopsKIC 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git LOOP start: 145 stop: 155 cut: 150 size: 11 skip rate: 0 extended?: False FOLD_TREE EDGE 1 144 -1 EDGE 144 150 -1 EDGE 144 156 1 EDGE 156 151 -1 EDGE 156 164 -1 setting up movers building random loop conformation with ideal bond lengths, bond angles, and omega angles using KIC attempt 0...succeeded. centroid stage loop KIC remodeling centroid stage loop rmsd to starting loop: 6.509848 high-res KIC refinement outputting decoy .test_kic.pdb core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -run:test_cycles True -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.15788 seconds. core.import_pose.import_pose: File '../test/data/2cpl_min.pdb' automatically determined to be of type PDB basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop protocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 144 -1 EDGE 144 150 -1 EDGE 144 156 1 EDGE 156 151 -1 EDGE 156 164 -1 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.018925 seconds. core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 3 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2 basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.223061 seconds to load from binary core.pack.pack_rotamers: built 1908 rotamers at 164 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine init temp: 1.5 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine final temp: 0.5 core.pack.task: Packer task: initialize from command line() protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: Not designing core.pack.pack_rotamers: built 1123 rotamers at 44 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -368.432 -368.432 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 1 -368.432 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 1/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.2083 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -378.23 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.21809 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -385.696 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 2/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 3/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.22069 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -385.961 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.23099 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -388.721 core.pack.pack_rotamers: built 1010 rotamers at 44 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -388.751 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -388.752 -388.752 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -388.752 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 2 -387.79 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 1/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.23853 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -387.783 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 2/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.39798 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -386.913 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 3/3 core.pack.pack_rotamers: built 993 rotamers at 44 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -386.95 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -386.953 -387.79 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -386.953 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 3 -386.828 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 1/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 3.00362 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -390.438 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 2/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 3/3 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.97232 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -390.652 core.pack.pack_rotamers: built 1018 rotamers at 44 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -391.58 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -391.593 -391.593 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -391.593 protocols.moves.TrialCounter: kic_refine_r1 trials= 8; accepts= 0.6250; energy_drop/trial= -1.59952 protocols.moves.TrialCounter: kic_refine_r2 trials= 9; accepts= 0.3333; energy_drop/trial= -1.16001 protocols.moves.TrialCounter: repack trials= 4; accepts= 1.0000; energy_drop/trial= -59.86967 Finished T650_LoopsKIC in 0:00:18.817540

mac.clang.python310.PyRosetta.unit.T660_LoopBuilding 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.11142 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB protocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.255818 seconds to load from binary protocols.loops.loops_main: Added cutpoint variant to residue 75 protocols.loops.loops_main: Added cutpoint variant to residue 76 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1201 rotamers at 44 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 649.218 649.218 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 1 649.218 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 585.944 585.944 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.737 583.737 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.328 583.328 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.519 583.328 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.189 583.189 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.669 582.669 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.527 582.669 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.69 582.669 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.412 582.412 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.412 582.412 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.663 581.663 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.111 581.111 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.071 581.071 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.612 580.612 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.696 580.612 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.19 580.19 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.842 579.842 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.628 579.628 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.232 579.232 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.633 579.232 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1088 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.633 579.232 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 2 579.69 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.214 579.69 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.045 579.69 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.954 579.69 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.025 579.69 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.806 579.69 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.806 579.69 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.642 579.642 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.666 579.642 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.768 579.642 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.759 579.642 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.459 579.459 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.164 579.164 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.243 579.164 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.184 579.164 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.189 579.164 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.137 579.137 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.237 579.137 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.145 579.137 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.342 579.137 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.151 579.137 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1076 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.15 579.137 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 3 579.284 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.224 579.224 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.224 579.224 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.218 579.218 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.907 578.907 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.811 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.811 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.014 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.44 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.44 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.928 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.847 578.811 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.708 578.708 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.352 578.352 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.352 578.352 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.321 578.321 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.233 578.233 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.284 578.233 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.229 578.229 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.234 578.229 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.226 578.226 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1070 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.226 578.226 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 4 578.348 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.348 578.348 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.52 578.348 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.797 578.348 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.573 578.348 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.066 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.108 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.108 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.256 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.793 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.649 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.499 578.066 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.972 577.972 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.821 577.821 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.468 577.468 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.468 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.021 577.468 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1065 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.021 577.468 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 5 577.556 protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 1/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.269 577.556 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.76 577.556 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.76 577.556 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.76 577.556 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.895 577.556 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.474 577.474 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.474 577.474 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.345 577.345 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.345 577.345 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.604 577.345 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.396 577.345 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.216 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.274 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.299 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for S┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Loop building -------------------------------------------------- FOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 mallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.252 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.273 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.273 577.216 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.191 577.191 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.295 577.191 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.306 577.191 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1086 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.306 577.191 protocols.moves.TrialCounter: repack trials= 6; accepts= 1.0000; energy_drop/trial= -50.02512 protocols.moves.TrialCounter: shear_ccd_min trials= 50; accepts= 0.8600; energy_drop/trial= -0.15222 protocols.moves.TrialCounter: small_ccd_min trials= 50; accepts= 0.8200; energy_drop/trial= -1.28296 Finished T660_LoopBuilding in 0:00:52.414121

mac.clang.python310.PyRosetta.unit.T700_FoldTree 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Fold tree -------------------------------------------------- FOLD_TREE EDGE 1 116 -1 FOLD_TREE EDGE 1 30 -1 EDGE 30 40 -1 EDGE 30 50 1 EDGE 50 116 -1 EDGE 50 41 -1 116 5 1 FOLD_TREE EDGE 1 30 -1 EDGE 30 40 -1 EDGE 30 50 1 EDGE 50 41 -1 EDGE 50 116 -1 FOLD_TREE core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.12931 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB Finished T700_FoldTree in 0:00:03.877605

mac.clang.python310.PyRosetta.unit.T800_ClassicRelax 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git testing ClassicRelax core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.07082 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop protocols.relax.ClassicRelax: Setting up default relax setting basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.22693 seconds to load from binary protocols.relax.ClassicRelax: protocols.relax.ClassicRelax: protocols.relax.ClassicRelax: =================================================================== protocols.relax.ClassicRelax: Stage 1 protocols.relax.ClassicRelax: Ramping repulsives with 3 outer cycles and 3 inner cycles core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 4003 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 3603 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 3138 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 3063 rotamers at 116 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.relax.ClassicRelax: protocols.relax.ClassicRelax: =================================================================== protocols.relax.ClassicRelax: Stage 2 protocols.relax.ClassicRelax: Mainmintrial for 10 with a full repack every 100 cycles core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.relax.ClassicRelax: protocols.relax.ClassicRelax: =================================================================== protocols.relax.ClassicRelax: Stage 3 protocols.relax.ClassicRelax: Mainmintrial for 10 core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.relax.ClassicRelax: Finished T800_ClassicRelax in 0:00:40.261225

mac.clang.python310.PyRosetta.unit.T850_SubClassing 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 Base::Base() ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git A.__init__... PyValue.__init__... A.foo_int(1) A.foo_value(wrong...) A.foo_string(qwerty) New Value[1]: A.foo_value! A.foo_value(wrong...) New Value[2]: A.foo_value! A.foo_value_sp(wrong...) New Value[3]: A.foo_value_sp! A.foo_int(1) A.foo_value(wrong...) A.foo_string(qwerty) New Value[4]: A.foo_value! A.foo_int(1) A.foo_value(wrong...) A.foo_string(qwerty) New Value[5]: A.foo_value! rosetta.utility.py.OverloadTest Test ----------------------- OverloadTest::self_test_virtual_p... Calling test(Value *v)... Calling test(Value *v)... Done! OverloadTest::self_test_virtual_p... Done! OverloadTest::self_test_virtual_ref... Calling test(Value &v)... Calling test(Value &v)... Done! OverloadTest::self_test_virtual_ref... Done! PyOverloadTest Test ----------------------------------------- OverloadTest::self_test_virtual_p... Calling test(Value *v)... Calling test(Value *v)... Done! OverloadTest::self_test_virtual_p... Done! OverloadTest::self_pure_test_virtual_p... Calling pure_test(Value *v)... Calling pure_test(Value *v)... Done! OverloadTest::self_pure_test_virtual_p... Done! OverloadTest::self_test_virtual_ref... Calling test(Value &v)... Calling test(Value &v)... Done! OverloadTest::self_test_virtual_ref... Done! OverloadTest::self_pure_test_virtual_ref... Calling pure_test(Value &v)... Calling pure_test(Value &v)... Done! OverloadTest::self_pure_test_virtual_ref... Done! PyOverloadTest.test_p(Value('unknown') ) PyOverloadTest.pure_test_p(Value('unknown') ) PyOverloadTest.test_ref(Value('unknown') ) PyOverloadTest.pure_test_ref(Value('unknown') ) My_New_Mover.__init__... My_New_Mover.apply: <class 'pyrosetta.rosetta.core.pose.Pose'> This My_New_Mover apply... Old phi=0.0, new phi=1.54 MyNewCI1B::__init__! --------------------------------------------- Score: 232.0 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.09352 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB Value destructor! [A.foo_value_sp!] Value destructor! [A.foo_value!] Value destructor! [unknown] Value destructor! [unknown] Finished T850_SubClassing in 0:00:03.790342

mac.clang.python310.PyRosetta.unit.T860_SubClassing_EnergyMethods 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git --------------------------------------------- MyCI1B_Method Score: 232.0 protocols.moves.MonteCarlo: "Temperature" (kT): 1 Total Trials: 0 Lowest Score: 232 Last Accepted Score: 232 last_accept = 232 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.04631 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB Finished T860_SubClassing_EnergyMethods in 0:00:03.881239

mac.clang.python310.PyRosetta.unit.T870_SubClassing_EnergyMethods2 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git --------------------------------------------- CI1B_Method Score: 232.0 --------------------------------------------- CI2B_Method Score: 525.0 --------------------------------------------- CD2B_Method Score: 525.0 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.11352 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T870_SubClassing_EnergyMethods2.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.core.scoring.methods import ContextIndependentOneBodyEnergy, ContextIndependentTwoBodyEnergy, ContextDependentTwoBodyEnergy Finished T870_SubClassing_EnergyMethods2 in 0:00:03.819345

mac.clang.python310.PyRosetta.unit.T880_Other 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git testing ligand modeling testing DNA modeling Done! core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.05196 seconds. core.import_pose.import_pose: File '../test/data/ligand_test.pdb' automatically determined to be of type PDB core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.229337 seconds to load from binary core.import_pose.import_pose: File '../test/data/dna_test.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name O5* to O5' core.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name C5* to C5' core.io.pose_from_sfr.PoseFromSFRBuilder: Number of nucleic acid residue fixups exceeds output limit. Rerun with -show_all_fixes to show everything. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: -12 C DG GUA:VirtualDNAPhosphate core.io.pose_from_sfr.PoseFromSFRBuilder: missing: P core.io.pose_from_sfr.PoseFromSFRBuilder: missing: O5' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C5' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C4' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C3' core.io.pose_from_sfr.PoseFromSFRBuilder: missing: O3' core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 164 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 166 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 167 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 169 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 170 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 172 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 173 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 174 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:UpperRNA:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 175 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE:LowerDNA:VirtualDNAPhosphate core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 177 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 181 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 182 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 183 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 184 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 185 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 186 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT:UpperDNA core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for OP1 and OP2 for residue DT core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue DT core.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: N9 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N7 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: C8 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162 core.conformation.Conformation: Connecting residues: 162 ( GUA:LowerDNA:VirtualDNAPhosphate ) and 163 ( CYT ) at atoms O3' and P core.conformation.Conformation: with mutual distances: 0.293633 and 0.00610344 core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 163 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 164 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 165 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 166 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 167 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 168 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 169 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 170 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 171 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 172 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 173 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 174 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 175 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 176 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 177 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 178 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 179 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 181 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 182 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 183 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 184 atom 2H2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 185 atom 2H2' (trying to store temperature in PDBInfo) core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 12 atom name N9 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph Finished T880_Other in 0:00:07.023528

mac.clang.python310.PyRosetta.unit.T900_distributed 「click to collapse/expand」

Unsupported python version for pyrosetta.distributed: sys.version_info(major=3, minor=10, micro=10, releaselevel='final', serial=0) Finished T900_distributed in 0:00:00.033965

mac.clang.python310.PyRosetta.unit.Workshop2test 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git PDB file name: ../test/data/workshops/1YY8.clean.pdb Total residues: 868 Sequence: DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS Fold tree: FOLD_TREE EDGE 1 213 -1 EDGE 1 214 1 EDGE 214 434 -1 EDGE 1 435 2 EDGE 435 647 -1 EDGE 1 648 3 EDGE 648 868 -1 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS Protein has 868 residues. GLY C 66 100 25 A 1 9 17 25 33 41 49 57 65 73 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVES LLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLH 81 89 97 105 113 121 129 137 145 153 EDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ HHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLLEEEEEELLEELLLLEE 161 169 177 185 193 201 209 217 225 233 ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGF EEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEELLLLLLLEEEEEELLLLLEEEELLLEEELLLLLEEEEEEEELL 241 249 257 265 273 281 289 297 305 313 SLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFA LLLLLLEEEEEELLLLLEEEEEEELLLLLEEELHHHLLLEEEEEELLLLEEEEEELLLLHHHLEEEEEEEELLLLLLLEE 321 329 337 345 353 361 369 377 385 393 YWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV EELLLEEEEELLLLLELLEEEEELLLHHHEEHHEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEE 401 409 417 425 433 441 449 457 465 473 VTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRL EEEEHHHLLLLLLEEEEEEHHHLEEEEEELLLLLLLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEE 481 489 497 505 513 521 529 537 545 553 LIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLK EEELLLEELLLLLLLEEEEEELLEEEEEELLLLHHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHH 561 569 577 585 593 601 609 617 625 633 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVT HLEEEEEEEEEEEELLLEEEEEEELLEEELLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEEELLLLLLEE 641 649 657 665 673 681 689 697 705 713 KSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDN EEEELLLLLEEEELLLEEELLLLLEEEEEEEELLLLLLLLEEEEEELLLLLEEEEEEELLLLLEEELHHHLLLEEEEEEL 721 729 737 745 753 761 769 777 785 793 SKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP LLLEEEEEELLLLHHHLEEEEEEEELLLLLLLEEEELLLEEEEELLLLLELLEEEEELLLHHHEEHHEEEEEEEEEEEEL 801 809 817 825 833 841 849 857 865 EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS LLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHHHLLLLEEEEEEHHHLEEEEEELLLLL -112.78988533697459 119.19490144825456 -59.969147488992036 1.4632323807242649 1.5092534578393384 <bound method PyCapsule.norm of <pyrosetta.rosetta.numeric.xyzVector_double_t object at 0x111f46d30>> 1.887434528690777 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.01634 seconds. core.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: Found disulfide between residues 235 308 core.conformation.Conformation: Found disulfide between residues 359 415 core.conformation.Conformation: Found disulfide between residues 457 522 core.conformation.Conformation: Found disulfide between residues 568 628 core.conformation.Conformation: Found disulfide between residues 669 742 core.conformation.Conformation: Found disulfide between residues 793 849 core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.217347 seconds to load from binary core.pack.pack_rotamers: built 85 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph Finished Workshop2test in 0:00:07.402150

mac.clang.python310.PyRosetta.unit.Workshop3test 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.02147 seconds. core.import_pose.import_pose: File '../test/data/workshops/6Q21.clean.pdb' automatically determined to be of type PDB core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.203326 seconds to load from binary core.scoring.ScoreFunction: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -4241.897 -4241.897 fa_rep 0.550 4336.454 2385.050 fa_sol 1.000 2798.424 2798.424 fa_intra_rep 0.005 3035.687 15.178 fa_intra_sol_xover4 1.000 180.944 180.944 lk_ball_wtd 1.000 -56.460 -56.460 fa_elec 1.000 -933.702 -933.702 pro_close 1.250 270.565 338.206 hbond_sr_bb 1.000 -181.224 -181.224 hbond_lr_bb 1.000 -130.586 -130.586 hbond_bb_sc 1.000 -58.168 -58.168 hbond_sc 1.000 -38.850 -38.850 dslf_fa13 1.250 0.000 0.000 omega 0.400 149.145 59.658 fa_dun 0.700 4635.733 3245.013 p_aa_pp 0.600 -101.427 -60.856 yhh_planarity 0.625 0.000 0.000 ref 1.000 188.455 188.455 rama_prepro 0.450 591.830 266.324 --------------------------------------------------- Total weighted score: 3775.512 core.scoring.Energies: E fa_atr fa_rep fa_sol fa_intra_repfa_intra_sol_x lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref rama_prepro core.scoring.Energies: E(i) 24 -7.40 19.03 2.94 8.76 0.09 -0.11 -0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.12 2.68 0.06 0.00 2.30 3.58 core.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy core.scoring.hbonds.HBondSet: #A 1 MET N B 162 GLU OE1 1.87 152.3 115.2 157.1 1.000 -1.850 core.scoring.hbonds.HBondSet: #A 1 MET N B 165 GLN OE1 1.59 159.1 136.2 147.7 0.859 -1.567 core.scoring.hbonds.HBondSet: #A 52 LEU N A 2 THR O 1.59 171.0 149.6 134.7 1.000 -0.439 core.scoring.hbonds.HBondSet: #A 2 THR N A 50 THR O 2.01 158.3 155.0 -175.7 1.000 -1.342 core.scoring.hbonds.HBondSet: #A 4 TYR N A 52 LEU O 1.71 146.0 157.4 151.1 1.000 -0.468 core.scoring.hbonds.HBondSet: #A 54 ASP N A 4 TYR O 1.72 151.1 150.2 49.0 1.000 -0.601 core.scoring.hbonds.HBondSet: #A 5 LYS N A 76 GLU OE1 1.52 175.1 149.4 13.9 0.765 -1.324 core.scoring.hbonds.HBondSet: #A 76 GLU N A 5 LYS O 1.97 142.0 123.6 -73.8 1.000 -0.616 core.scoring.hbonds.HBondSet: #A 77 GLY N A 5 LYS O 2.16 141.0 146.4 -155.0 1.000 -0.989 core.scoring.hbonds.HBondSet: #A 6 LEU N A 54 ASP O 1.88 169.2 151.8 102.5 1.000 -1.038 core.scoring.hbonds.HBondSet: #A 56 LEU N A 6 LEU O 2.05 163.6 163.5 167.1 1.000 -1.200 core.scoring.hbonds.HBondSet: #A 7 VAL N A 77 GLY O 1.65 159.9 148.6 -140.0 1.000 -0.669 core.scoring.hbonds.HBondSet: #A 8 VAL N A 56 LEU O 2.14 166.5 145.2 73.7 1.000 -1.058 core.scoring.hbonds.HBondSet: #A 58 THR N A 8 VAL O 2.66 140.8 137.3 32.0 1.000 -0.139 core.scoring.hbonds.HBondSet: #A 81 VAL N A 9 VAL O 1.76 166.8 144.1 -124.3 1.000 -0.996 core.scoring.hbonds.HBondSet: #A 9 VAL N A 79 LEU O 1.98 138.4 151.4 57.5 1.000 -0.592 core.scoring.hbonds.HBondSet: #A 14 VAL N A 11 ALA O 1.88 154.8 146.6 -154.7 1.000 -1.324 core.scoring.hbonds.HBondSet: #A 117 LYS NZ A 13 GLY O 2.09 158.9 168.0 43.3 0.929 -0.307 core.scoring.hbonds.HBondSet: #A 116 ASN ND2A 14 VAL O 2.17 167.3 134.9 147.9 1.000 -1.433 core.scoring.hbonds.HBondSet: #A 19 LEU N A 15 GLY O 1.86 152.2 155.7 -122.2 1.000 -0.811 core.scoring.hbonds.HBondSet: #A 20 THR N A 16 LYS O 1.90 177.7 161.6 -167.9 1.000 -1.327 core.scoring.hbonds.HBondSet: #A 21 ILE N A 17 SER O 1.81 151.9 161.2 83.6 1.000 -0.613 core.scoring.hbonds.HBondSet: #A 17 SER OG A 57 ASP OD2 1.82 126.8 115.0 -166.4 1.000 -0.827 core.scoring.hbonds.HBondSet: #A 22 GLN N A 18 ALA O 2.31 140.8 122.1 -104.6 1.000 -0.323 core.scoring.hbonds.HBondSet: #A 23 LEU N A 19 LEU O 2.28 137.6 137.1 -174.9 1.000 -1.131 core.scoring.hbonds.HBondSet: #A 23 LEU N A 20 THR O 1.97 123.1 112.5 -78.8 1.000 -0.055 core.scoring.hbonds.HBondSet: #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979 core.scoring.hbonds.HBondSet: #A 25 GLN N A 21 ILE O 2.24 105.4 127.6 -17.1 1.000 -0.432 core.scoring.hbonds.HBondSet: #A 149 ARG NH2A 22 GLN O 1.69 156.8 124.3 126.5 0.859 -0.895 core.scoring.hbonds.HBondSet: #A 30 ASP N A 31 GLU OE2 1.95 148.8 110.5 52.5 0.318 -1.124 core.scoring.hbonds.HBondSet: #A 57 ASP N A 38 ASP O 2.02 149.5 176.9 -58.1 1.000 -0.727 core.scoring.hbonds.HBondSet: #A 40 TYR N A 55 ILE O 2.06 133.0 125.1 62.1 1.000 -0.543 core.scoring.hbonds.HBondSet: #A 55 ILE N A 40 TYR O 1.69 157.5 167.5 -58.5 1.000 -0.451 core.scoring.hbonds.HBondSet: #A 42 LYS N A 53 LEU O 2.02 144.4 129.4 31.9 1.000 -1.371 core.scoring.hbonds.HBondSet: #A 53 LEU N A 42 LYS O 1.74 153.8 165.7 -34.7 1.000 -0.598 core.scoring.hbonds.HBondSet: #A 43 GLN NE2B 141 TYR O 1.70 166.6 150.3 33.2 0.859 -1.175 core.scoring.hbonds.HBondSet: #B 141 TYR N A 43 GLN OE1 2.24 131.2 99.3 -167.7 0.859 -0.219 core.scoring.hbonds.HBondSet: #A 44 VAL N A 51 CYS O 1.71 163.4 149.6 -1.3 1.000 -1.165 core.scoring.hbonds.HBondSet: #A 46 ILE N A 49 GLU O 2.07 141.6 134.8 -34.7 1.000 -1.178 core.scoring.hbonds.HBondSet: #A 49 GLU N A 46 ILE O 2.22 146.3 99.6 95.0 1.000 -0.222 core.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD1 2.30 127.4 91.6 172.3 0.718 -0.063 core.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD2 2.37 163.9 86.4 -172.5 0.718 -0.412 core.scoring.hbonds.HBondSet: #A 164 ARG NH1A 47 ASP OD2 1.48 142.3 122.9 -33.8 0.671 -0.468 core.scoring.hbonds.HBondSet: #A 164 ARG NH2A 47 ASP OD2 1.87 128.8 120.1 73.7 0.671 -0.154 core.scoring.hbonds.HBondSet: #B 169 ARG NH1A 49 GLU OE2 1.85 136.1 126.0 132.0 0.624 -0.645 core.scoring.hbonds.HBondSet: #B 169 ARG NH2A 49 GLU OE2 2.28 126.2 161.1 -104.1 0.624 -0.007 core.scoring.hbonds.HBondSet: #A 58 THR N A 56 LEU O 2.50 117.5 111.9 -148.7 1.000 -0.051 core.scoring.hbonds.HBondSet: #A 65 SER N A 63 GLU OE1 1.63 154.5 118.5 115.9 0.224 -0.884 core.scoring.hbonds.HBondSet: #A 68 ARG NH2A 96 TYR OH 1.81 164.5 113.9 -150.2 0.788 -1.692 core.scoring.hbonds.HBondSet: #A 74 THR OG1A 71 TYR O 2.00 159.3 114.5 -39.3 0.576 -0.378 core.scoring.hbonds.HBondSet: #A 71 TYR N A 72 MET O 2.18 108.7 111.7 7.3 1.000 -0.617 core.scoring.hbonds.HBondSet: #A 75 GLY N A 71 TYR O 1.64 137.5 150.1 -159.0 1.000 -0.191 core.scoring.hbonds.HBondSet: #A 104 LYS NZ A 75 GLY O 1.73 151.1 175.2 27.0 0.788 -0.427 core.scoring.hbonds.HBondSet: #A 112 VAL N A 78 PHE O 2.25 148.8 157.4 173.4 1.000 -0.878 core.scoring.hbonds.HBondSet: #A 78 PHE N A 110 PRO O 2.01 158.7 153.2 -144.4 1.000 -1.242 core.scoring.hbonds.HBondSet: #A 80 CYS N A 112 VAL O 2.27 143.1 149.0 68.7 1.000 -0.434 core.scoring.hbonds.HBondSet: #A 114 VAL N A 80 CYS O 2.23 169.9 156.5 101.6 1.000 -0.960 core.scoring.hbonds.HBondSet: #A 116 ASN N A 82 PHE O 1.76 152.5 166.5 -98.5 1.000 -0.518 core.scoring.hbonds.HBondSet: #A 82 PHE N A 114 VAL O 2.14 145.0 155.1 -96.1 1.000 -0.561 core.scoring.hbonds.HBondSet: #A 86 ASN N A 83 ALA O 2.32 149.5 107.5 -109.9 1.000 -0.454 core.scoring.hbonds.HBondSet: #A 83 ALA N A 89 SER OG 1.92 159.9 113.0 146.0 1.000 -2.159 core.scoring.hbonds.HBondSet: #A 84 ILE N A 116 ASN O 2.25 158.9 161.3 -45.4 1.000 -0.878 core.scoring.hbonds.HBondSet: #A 124 THR N A 84 ILE O 1.65 177.5 159.1 166.1 1.000 -0.788 core.scoring.hbonds.HBondSet: #A 88 LYS N A 86 ASN OD1 1.96 146.5 130.0 -97.6 0.600 -0.800 core.scoring.hbonds.HBondSet: #A 90 PHE N A 86 ASN O 2.39 155.4 153.6 -141.6 1.000 -0.744 core.scoring.hbonds.HBondSet: #A 91 GLU N A 87 THR O 2.43 136.5 134.7 -143.4 1.000 -0.557 core.scoring.hbonds.HBondSet: #A 92 ASP N A 88 LYS O 2.28 145.5 141.1 -118.0 1.000 -0.589 core.scoring.hbonds.HBondSet: #A 96 TYR N A 92 ASP O 2.47 148.2 144.3 139.2 1.000 -0.571 core.scoring.hbonds.HBondSet: #A 95 GLN N A 92 ASP O 1.65 147.8 124.5 -102.5 1.000 -0.067 core.scoring.hbonds.HBondSet: #A 97 ARG N A 93 ILE O 2.13 156.0 164.2 -73.0 1.000 -0.838 core.scoring.hbonds.HBondSet: #A 98 GLU N A 94 HIS O 2.17 155.1 127.3 -111.1 1.000 -0.919 core.scoring.hbonds.HBondSet: #A 99 GLN N A 95 GLN O 2.20 147.3 151.5 -140.0 1.000 -0.869 core.scoring.hbonds.HBondSet: #A 100 ILE N A 96 TYR O 2.07 160.1 159.6 177.7 1.000 -1.238 core.scoring.hbonds.HBondSet: #A 101 LYS N A 97 ARG O 2.17 173.1 164.2 -178.2 1.000 -1.217 core.scoring.hbonds.HBondSet: #A 102 ARG N A 98 GLU O 2.38 139.0 138.2 -136.4 1.000 -0.549 core.scoring.hbonds.HBondSet: #A 103 VAL N A 99 GLN O 1.71 166.8 162.3 -144.5 1.000 -0.762 core.scoring.hbonds.HBondSet: #A 104 LYS N A 100 ILE O 1.67 160.9 170.6 -154.6 1.000 -0.436 core.scoring.hbonds.HBondSet: #A 105 ASP N A 102 ARG O 2.25 143.4 93.6 -86.8 1.000 -0.002 core.scoring.hbonds.HBondSet: #A 108 ASP N A 106 SER OG 1.97 152.0 90.6 86.3 0.365 -1.113 core.scoring.hbonds.HBondSet: #A 113 LEU N A 140 PRO O 1.81 148.3 171.8 67.9 1.000 -0.521 core.scoring.hbonds.HBondSet: #A 142 ILE N A 113 LEU O 1.79 150.9 160.0 151.3 1.000 -0.770 core.scoring.hbonds.HBondSet: #A 115 GLY N A 142 ILE O 2.24 157.4 135.9 129.0 1.000 -1.120 core.scoring.hbonds.HBondSet: #A 144 THR N A 115 GLY O 2.13 162.0 119.4 101.2 1.000 -0.987 core.scoring.hbonds.HBondSet: #A 117 LYS N A 116 ASN OD1 1.85 141.7 101.3 -66.8 1.000 -0.539 core.scoring.hbonds.HBondSet: #A 120 LEU N A 117 LYS O 1.95 172.9 143.4 -107.1 1.000 -1.171 core.scoring.hbonds.HBondSet: #A 117 LYS N A 144 THR O 2.01 106.8 129.9 -132.7 1.000 -0.125 core.scoring.hbonds.HBondSet: #A 118 CYS N A 144 THR O 1.90 170.5 123.4 123.6 1.000 -1.398 core.scoring.hbonds.HBondSet: #A 123 ARG NH1A 143 GLU OE2 1.95 158.1 107.0 -145.0 0.741 -1.215 core.scoring.hbonds.HBondSet: #A 123 ARG NH2A 143 GLU OE1 1.63 171.8 119.9 158.6 0.741 -1.303 core.scoring.hbonds.HBondSet: #A 123 ARG NH1A 125 VAL O 2.02 173.1 148.1 -124.0 0.694 -1.007 core.scoring.hbonds.HBondSet: #A 130 ALA N A 126 GLU O 1.87 158.8 152.0 -177.9 1.000 -1.364 core.scoring.hbonds.HBondSet: #A 132 ASP N A 128 ARG O 2.21 150.7 138.4 -109.6 1.000 -0.724 core.scoring.hbonds.HBondSet: #A 133 LEU N A 129 GLN O 2.28 151.1 146.3 -142.0 1.000 -0.960 core.scoring.hbonds.HBondSet: #A 134 ALA N A 130 ALA O 1.79 166.2 162.7 -178.5 1.000 -1.051 core.scoring.hbonds.HBondSet: #A 135 ARG N A 131 GLN O 1.83 166.3 155.5 -99.9 1.000 -0.923 core.scoring.hbonds.HBondSet: #A 136 SER N A 132 ASP O 1.78 156.7 145.2 -115.7 1.000 -0.779 core.scoring.hbonds.HBondSet: #A 137 TYR N A 133 LEU O 1.92 158.6 154.8 -155.1 1.000 -1.247 core.scoring.hbonds.HBondSet: #A 138 GLY N A 134 ALA O 1.83 121.8 139.0 -163.6 1.000 -0.700 core.scoring.hbonds.HBondSet: #A 139 ILE N A 134 ALA O 2.24 163.7 126.8 83.5 1.000 -0.871 core.scoring.hbonds.HBondSet: #A 141 TYR OH A 143 GLU OE2 1.54 139.3 111.7 0.2 0.953 -1.165 core.scoring.hbonds.HBondSet: #A 141 TYR N C 43 GLN OE1 2.08 161.9 118.7 -172.1 0.835 -2.242 core.scoring.hbonds.HBondSet: #C 43 GLN NE2A 141 TYR O 2.33 146.4 124.9 79.1 0.835 -0.190 core.scoring.hbonds.HBondSet: #A 148 THR N A 145 SER OG 2.05 157.6 137.3 -91.6 0.694 -1.629 core.scoring.hbonds.HBondSet: #A 145 SER N A 150 GLN O 2.02 170.9 150.4 -53.6 1.000 -1.299 core.scoring.hbonds.HBondSet: #A 150 GLN N A 148 THR OG1 2.60 158.2 106.0 37.4 0.553 -0.009 core.scoring.hbonds.HBondSet: #A 152 VAL N A 149 ARG O 2.41 170.1 119.9 -103.6 1.000 -0.718 core.scoring.hbonds.HBondSet: #A 149 ARG NH2A 153 GLU OE2 2.57 140.9 135.9 23.0 0.671 -0.460 core.scoring.hbonds.HBondSet: #A 155 ALA N A 151 GLY O 2.17 152.2 149.8 -130.5 1.000 -0.948 core.scoring.hbonds.HBondSet: #A 156 PHE N A 152 VAL O 2.47 167.0 144.2 -123.9 1.000 -0.728 core.scoring.hbonds.HBondSet: #A 157 TYR N A 153 GLU O 1.72 169.3 166.5 -179.4 1.000 -0.834 core.scoring.hbonds.HBondSet: #A 157 TYR OH A 153 GLU OE1 2.17 146.9 99.0 117.3 0.765 -0.012 core.scoring.hbonds.HBondSet: #A 158 THR N A 154 ASP O 1.89 147.3 139.5 -98.2 1.000 -0.633 core.scoring.hbonds.HBondSet: #A 159 LEU N A 155 ALA O 2.17 148.5 137.9 -132.2 1.000 -1.027 core.scoring.hbonds.HBondSet: #A 160 VAL N A 156 PHE O 2.05 159.9 143.0 -132.0 1.000 -1.295 core.scoring.hbonds.HBondSet: #A 161 ARG N A 157 TYR O 1.81 160.4 153.3 -118.9 1.000 -0.892 core.scoring.hbonds.HBondSet: #A 162 GLU N A 158 THR O 2.08 152.2 148.4 -125.7 1.000 -0.984 core.scoring.hbonds.HBondSet: #A 163 ILE N A 159 LEU O 2.04 159.2 154.3 -135.6 1.000 -1.160 core.scoring.hbonds.HBondSet: #A 164 ARG N A 160 VAL O 1.82 170.5 164.7 -100.1 1.000 -0.943 core.scoring.hbonds.HBondSet: #A 165 GLN N A 161 ARG O 1.77 162.3 145.7 -126.0 1.000 -0.962 core.scoring.hbonds.HBondSet: #C 1 MET N A 162 GLU OE2 1.52 173.9 111.2 -150.8 0.859 -1.532 core.scoring.hbonds.HBondSet: #A 166 HIS N A 162 GLU O 1.67 153.5 143.8 -117.4 1.000 -0.382 core.scoring.hbonds.HBondSet: #A 167 LYS N A 163 ILE O 1.81 160.2 169.3 -164.8 1.000 -0.852 core.scoring.hbonds.HBondSet: #C 1 MET N A 165 GLN OE1 1.68 168.3 116.6 -140.8 0.694 -1.841 core.scoring.hbonds.HBondSet: #A 168 LEU N A 165 GLN O 2.16 161.1 119.3 -109.5 1.000 -1.021 core.scoring.hbonds.HBondSet: #A 169 ARG N A 167 LYS O 2.09 119.4 111.3 -127.2 1.000 -0.278 core.scoring.hbonds.HBondSet: #A 169 ARG N A 171 LEU O 2.31 134.6 103.8 72.2 1.000 -0.014 core.scoring.hbonds.HBondSet: #B 1 MET N D 162 GLU OE2 1.78 162.3 101.4 -153.1 0.953 -1.514 core.scoring.hbonds.HBondSet: #B 1 MET N D 165 GLN OE1 2.24 168.6 123.5 -111.6 0.741 -0.769 core.scoring.hbonds.HBondSet: #B 52 LEU N B 2 THR O 1.61 169.6 162.9 148.4 1.000 -0.412 core.scoring.hbonds.HBondSet: #B 2 THR N B 50 THR O 2.03 162.9 155.5 -160.6 1.000 -1.366 core.scoring.hbonds.HBondSet: #B 4 TYR N B 52 LEU O 1.80 164.8 167.3 95.8 1.000 -0.828 core.scoring.hbonds.HBondSet: #B 54 ASP N B 4 TYR O 1.94 154.4 155.9 57.8 1.000 -0.931 core.scoring.hbonds.HBondSet: #B 4 TYR OH B 49 GLU OE1 1.84 151.6 105.5 143.8 0.812 -0.974 core.scoring.hbonds.HBondSet: #B 5 LYS N B 76 GLU OE1 1.53 174.9 152.7 -34.8 0.765 -1.099 core.scoring.hbonds.HBondSet: #B 76 GLU N B 5 LYS O 1.69 161.1 146.8 -26.4 1.000 -1.018 core.scoring.hbonds.HBondSet: #B 77 GLY N B 5 LYS O 2.40 143.5 155.6 146.2 1.000 -0.432 core.scoring.hbonds.HBondSet: #B 6 LEU N B 54 ASP O 2.00 144.1 139.4 96.3 1.000 -0.600 core.scoring.hbonds.HBondSet: #B 56 LEU N B 6 LEU O 1.66 162.8 157.9 174.1 1.000 -0.718 core.scoring.hbonds.HBondSet: #B 79 LEU N B 7 VAL O 1.74 157.3 152.8 147.5 1.000 -0.891 core.scoring.hbonds.HBondSet: #B 7 VAL N B 77 GLY O 2.02 174.4 161.6 166.4 1.000 -1.357 core.scoring.hbonds.HBondSet: #B 58 THR N B 8 VAL O 2.72 146.2 149.3 -11.1 1.000 -0.011 core.scoring.hbonds.HBondSet: #B 8 VAL N B 56 LEU O 1.97 177.7 162.1 69.5 1.000 -1.162 core.scoring.hbonds.HBondSet: #B 9 VAL N B 79 LEU O 1.99 152.6 143.2 57.5 1.000 -1.020 core.scoring.hbonds.HBondSet: #B 81 VAL N B 9 VAL O 1.91 177.5 153.5 -123.6 1.000 -1.243 core.scoring.hbonds.HBondSet: #B 14 VAL N B 11 ALA O 2.39 160.5 137.3 -127.2 1.000 -0.898 core.scoring.hbonds.HBondSet: #B 19 LEU N B 15 GLY O 1.91 147.7 148.4 -139.0 1.000 -0.998 core.scoring.hbonds.HBondSet: #B 20 THR N B 16 LYS O 1.82 178.0 165.1 -147.9 1.000 -1.102 core.scoring.hbonds.HBondSet: #B 21 ILE N B 17 SER O 1.94 143.6 134.8 -118.0 1.000 -0.775 core.scoring.hbonds.HBondSet: #B 17 SER OG B 57 ASP OD2 2.05 111.8 116.7 177.1 1.000 -0.366 core.scoring.hbonds.HBondSet: #B 22 GLN N B 18 ALA O 1.97 153.3 145.9 -100.8 1.000 -0.831 core.scoring.hbonds.HBondSet: #B 23 LEU N B 19 LEU O 2.30 169.7 154.3 -159.7 1.000 -1.230 core.scoring.hbonds.HBondSet: #B 24 ILE N B 20 THR O 2.14 171.9 143.2 -132.6 1.000 -1.403 core.scoring.hbonds.HBondSet: #B 25 GLN N B 21 ILE O 1.99 147.2 133.1 -81.7 1.000 -0.687 core.scoring.hbonds.HBondSet: #B 26 ASN N B 21 ILE O 2.58 123.3 138.4 -158.7 1.000 -0.044 core.scoring.hbonds.HBondSet: #B 26 ASN N B 22 GLN O 1.79 133.6 118.3 -62.9 1.000 -0.337 core.scoring.hbonds.HBondSet: #B 38 ASP N B 57 ASP O 1.85 160.4 146.8 -3.4 1.000 -1.515 core.scoring.hbonds.HBondSet: #B 57 ASP N B 38 ASP O 1.89 149.2 160.7 -105.2 1.000 -0.676 core.scoring.hbonds.HBondSet: #B 40 TYR N B 55 ILE O 2.11 143.2 150.5 52.1 1.000 -0.744 core.scoring.hbonds.HBondSet: #B 55 ILE N B 40 TYR O 2.12 137.4 137.0 -91.8 1.000 -0.380 core.scoring.hbonds.HBondSet: #B 42 LYS N B 53 LEU O 1.91 134.3 138.2 49.9 1.000 -0.670 core.scoring.hbonds.HBondSet: #B 44 VAL N B 51 CYS O 1.91 173.0 163.2 -19.0 1.000 -1.262 core.scoring.hbonds.HBondSet: #B 51 CYS N B 44 VAL O 1.70 159.6 163.0 112.3 1.000 -0.521 core.scoring.hbonds.HBondSet: #B 46 ILE N B 49 GLU O 1.89 149.1 141.5 15.9 1.000 -1.413 core.scoring.hbonds.HBondSet: #B 164 ARG NH2B 46 ILE O 1.91 143.8 123.3 -75.0 0.835 -0.513 core.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD2 2.06 128.7 100.1 -167.7 0.718 -0.614 core.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD1 1.97 118.9 114.3 145.6 0.718 -0.498 core.scoring.hbonds.HBondSet: #B 164 ARG NH1B 47 ASP OD2 1.52 144.2 128.2 -31.0 0.741 -0.595 core.scoring.hbonds.HBondSet: #B 164 ARG NE B 49 GLU OE1 2.22 142.9 142.9 -117.5 0.788 -0.542 core.scoring.hbonds.HBondSet: #B 164 ARG NH2B 49 GLU OE1 2.04 151.6 123.3 -27.3 0.788 -1.398 core.scoring.hbonds.HBondSet: #B 63 GLU N B 62 GLU OE2 2.31 142.0 107.1 -34.1 0.341 -0.378 core.scoring.hbonds.HBondSet: #B 68 ARG N B 64 TYR O 2.21 159.0 142.6 -170.1 1.000 -1.568 core.scoring.hbonds.HBondSet: #B 66 ALA N B 68 ARG O 2.47 136.1 106.6 33.2 1.000 -0.418 core.scoring.hbonds.HBondSet: #B 69 ASP N B 67 MET O 1.74 106.9 117.0 -154.2 1.000 -0.195 core.scoring.hbonds.HBondSet: #B 70 GLN N B 67 MET O 1.98 119.6 120.4 -45.6 1.000 -0.524 core.scoring.hbonds.HBondSet: #B 71 TYR N B 67 MET O 2.16 162.9 149.0 67.5 1.000 -1.022 core.scoring.hbonds.HBondSet: #B 73 ARG N B 69 ASP O 2.51 126.5 117.9 -129.1 1.000 -0.007 core.scoring.hbonds.HBondSet: #B 73 ARG NH2B 69 ASP OD1 2.57 139.8 133.2 -39.3 0.459 -0.260 core.scoring.hbonds.HBondSet: #B 74 THR N B 70 GLN O 2.49 146.7 125.7 -106.1 1.000 -0.149 core.scoring.hbonds.HBondSet: #B 75 GLY N B 71 TYR O 1.87 145.5 145.5 -114.3 1.000 -0.663 core.scoring.hbonds.HBondSet: #B 112 VAL N B 78 PHE O 2.16 146.2 176.3 179.0 1.000 -0.584 core.scoring.hbonds.HBondSet: #B 78 PHE N B 110 PRO O 2.04 158.2 134.9 -140.7 1.000 -1.502 core.scoring.hbonds.HBondSet: #B 114 VAL N B 80 CYS O 1.97 165.7 143.0 81.3 1.000 -1.057 core.scoring.hbonds.HBondSet: #B 80 CYS N B 112 VAL O 1.96 160.5 171.4 -82.6 1.000 -0.954 core.scoring.hbonds.HBondSet: #B 116 ASN N B 82 PHE O 2.01 161.1 144.6 -120.6 1.000 -1.162 core.scoring.hbonds.HBondSet: #B 86 ASN N B 83 ALA O 1.81 161.3 117.4 -107.2 1.000 -0.888 core.scoring.hbonds.HBondSet: #B 83 ALA N B 89 SER OG 1.96 171.4 124.8 149.0 1.000 -2.326 core.scoring.hbonds.HBondSet: #B 84 ILE N B 116 ASN O 1.99 170.8 165.9 28.4 1.000 -1.215 core.scoring.hbonds.HBondSet: #B 124 THR N B 84 ILE O 2.25 143.4 147.0 -164.4 1.000 -1.010 core.scoring.hbonds.HBondSet: #B 89 SER N B 86 ASN OD1 1.35 169.0 136.5 -89.4 0.929 -0.473 core.scoring.hbonds.HBondSet: #B 90 PHE N B 86 ASN O 2.39 149.6 128.9 -139.9 1.000 -0.954 core.scoring.hbonds.HBondSet: #B 87 THR OG1B 124 THR OG1 1.94 120.7 134.4 95.7 0.576 -0.105 core.scoring.hbonds.HBondSet: #B 91 GLU N B 87 THR O 1.86 159.4 146.8 -126.5 1.000 -1.080 core.scoring.hbonds.HBondSet: #B 92 ASP N B 88 LYS O 2.02 132.2 148.3 -133.4 1.000 -0.579 core.scoring.hbonds.HBondSet: #B 96 TYR N B 92 ASP O 2.17 155.0 146.9 149.5 1.000 -1.263 core.scoring.hbonds.HBondSet: #B 97 ARG N B 93 ILE O 2.00 161.9 151.3 -100.5 1.000 -1.005 core.scoring.hbonds.HBondSet: #B 98 GLU N B 94 HIS O 2.09 144.5 133.0 -121.8 1.000 -0.859 core.scoring.hbonds.HBondSet: #B 99 GLN N B 95 GLN O 1.75 174.2 171.9 -172.4 1.000 -0.848 core.scoring.hbonds.HBondSet: #B 100 ILE N B 96 TYR O 1.99 154.7 141.5 -129.9 1.000 -1.183 core.scoring.hbonds.HBondSet: #B 97 ARG NH1B 98 GLU OE1 2.08 102.1 136.3 167.3 0.600 -0.281 core.scoring.hbonds.HBondSet: #B 101 LYS N B 97 ARG O 2.20 169.3 146.3 -103.0 1.000 -1.010 core.scoring.hbonds.HBondSet: #B 102 ARG N B 98 GLU O 2.10 155.0 157.1 -125.1 1.000 -0.944 core.scoring.hbonds.HBondSet: #B 103 VAL N B 99 GLN O 2.07 144.8 153.9 -148.4 1.000 -0.924 core.scoring.hbonds.HBondSet: #B 104 LYS N B 101 LYS O 2.32 156.3 98.4 -104.6 1.000 -0.333 core.scoring.hbonds.HBondSet: #B 105 ASP N B 101 LYS O 1.87 114.7 134.2 -113.9 1.000 -0.001 core.scoring.hbonds.HBondSet: #B 106 SER N B 104 LYS O 2.12 146.8 90.6 135.1 1.000 -0.382 core.scoring.hbonds.HBondSet: #B 142 ILE N B 113 LEU O 2.29 151.5 148.5 168.3 1.000 -1.122 core.scoring.hbonds.HBondSet: #B 113 LEU N B 140 PRO O 2.26 166.9 142.6 -106.9 1.000 -0.939 core.scoring.hbonds.HBondSet: #B 115 GLY N B 142 ILE O 1.89 175.4 163.3 115.9 1.000 -1.115 core.scoring.hbonds.HBondSet: #B 144 THR N B 115 GLY O 1.82 166.4 143.8 108.2 1.000 -0.975 core.scoring.hbonds.HBondSet: #B 116 ASN ND2B 144 THR OG1 2.11 151.9 114.3 74.4 1.000 -1.625 core.scoring.hbonds.HBondSet: #B 120 LEU N B 117 LYS O 1.61 160.9 146.4 -148.9 1.000 -0.638 core.scoring.hbonds.HBondSet: #B 118 CYS N B 144 THR O 2.26 149.6 158.9 128.3 1.000 -0.664 core.scoring.hbonds.HBondSet: #B 122 ALA N B 120 LEU O 2.39 118.6 115.2 -135.1 1.000 -0.091 core.scoring.hbonds.HBondSet: #B 123 ARG NE B 125 VAL O 1.27 158.8 151.8 151.1 0.859 -0.468 core.scoring.hbonds.HBondSet: #B 123 ARG NH1B 143 GLU OE1 2.43 152.6 131.2 154.5 0.835 -1.002 core.scoring.hbonds.HBondSet: #B 123 ARG NH2B 143 GLU OE2 2.05 144.9 97.4 -150.9 0.835 -0.765 core.scoring.hbonds.HBondSet: #B 130 ALA N B 126 GLU O 2.05 144.5 148.6 -178.6 1.000 -1.206 core.scoring.hbonds.HBondSet: #B 126 GLU N B 129 GLN OE1 1.82 136.4 92.4 58.0 0.482 -0.121 core.scoring.hbonds.HBondSet: #B 129 GLN N B 126 GLU O 2.06 119.8 113.4 -80.2 1.000 -0.010 core.scoring.hbonds.HBondSet: #B 128 ARG NH2B 127 SER OG 1.74 118.8 110.7 98.3 0.435 -0.082 core.scoring.hbonds.HBondSet: #B 130 ALA N B 127 SER O 1.83 123.3 115.7 -86.8 1.000 -0.001 core.scoring.hbonds.HBondSet: #B 131 GLN N B 127 SER O 1.62 168.0 152.9 134.3 1.000 -0.522 core.scoring.hbonds.HBondSet: #B 132 ASP N B 128 ARG O 1.71 157.8 144.0 -118.8 1.000 -0.662 core.scoring.hbonds.HBondSet: #B 133 LEU N B 129 GLN O 2.33 152.8 121.1 -102.2 1.000 -0.556 core.scoring.hbonds.HBondSet: #B 134 ALA N B 130 ALA O 1.84 166.9 159.5 -175.0 1.000 -1.226 core.scoring.hbonds.HBondSet: #B 135 ARG N B 131 GLN O 1.92 146.8 146.1 -91.4 1.000 -0.623 core.scoring.hbonds.HBondSet: #B 136 SER N B 132 ASP O 2.11 155.5 152.5 -172.9 1.000 -1.320 core.scoring.hbonds.HBondSet: #B 137 TYR N B 133 LEU O 2.17 133.9 144.9 -123.0 1.000 -0.463 core.scoring.hbonds.HBondSet: #B 138 GLY N B 134 ALA O 1.85 135.9 139.4 -133.7 1.000 -0.690 core.scoring.hbonds.HBondSet: #B 139 ILE N B 134 ALA O 1.78 172.1 146.2 58.4 1.000 -1.059 core.scoring.hbonds.HBondSet: #B 141 TYR OH B 143 GLU OE2 1.30 169.7 124.0 -22.7 0.953 -1.194 core.scoring.hbonds.HBondSet: #B 149 ARG N B 145 SER O 1.85 110.9 146.3 -130.1 1.000 -0.001 core.scoring.hbonds.HBondSet: #B 148 THR N B 145 SER OG 2.10 165.0 108.1 -79.1 0.694 -2.084 core.scoring.hbonds.HBondSet: #B 145 SER N B 150 GLN O 1.80 163.2 158.2 -5.1 1.000 -1.148 core.scoring.hbonds.HBondSet: #B 150 GLN N B 148 THR OG1 2.31 163.9 114.4 48.9 0.576 -1.417 core.scoring.hbonds.HBondSet: #B 152 VAL N B 149 ARG O 2.57 162.8 114.6 -116.9 1.000 -0.414 core.scoring.hbonds.HBondSet: #B 155 ALA N B 151 GLY O 1.98 152.5 142.8 -118.1 1.000 -0.965 core.scoring.hbonds.HBondSet: #B 156 PHE N B 152 VAL O 2.52 168.0 149.9 -128.4 1.000 -0.636 core.scoring.hbonds.HBondSet: #B 157 TYR N B 153 GLU O 2.01 159.5 148.4 -101.6 1.000 -0.968 core.scoring.hbonds.HBondSet: #B 158 THR N B 154 ASP O 1.96 151.7 136.5 -81.7 1.000 -0.789 core.scoring.hbonds.HBondSet: #B 159 LEU N B 155 ALA O 2.49 137.7 130.1 -132.6 1.000 -0.327 core.scoring.hbonds.HBondSet: #B 160 VAL N B 156 PHE O 2.28 136.6 138.3 -137.9 1.000 -0.671 core.scoring.hbonds.HBondSet: #B 161 ARG N B 157 TYR O 2.05 160.9 147.4 -145.4 1.000 -1.405 core.scoring.hbonds.HBondSet: #B 162 GLU N B 158 THR O 1.98 142.2 135.1 -129.6 1.000 -0.935 core.scoring.hbonds.HBondSet: #B 163 ILE N B 159 LEU O 2.27 145.9 130.6 -115.9 1.000 -0.628 core.scoring.hbonds.HBondSet: #B 164 ARG N B 160 VAL O 1.87 170.6 168.8 -122.1 1.000 -1.038 core.scoring.hbonds.HBondSet: #B 165 GLN N B 161 ARG O 1.97 158.8 148.5 -96.5 1.000 -0.933 core.scoring.hbonds.HBondSet: #B 166 HIS N B 162 GLU O 2.15 141.4 126.0 -121.4 1.000 -0.756 core.scoring.hbonds.HBondSet: #B 167 LYS N B 163 ILE O 2.28 116.2 139.1 -144.3 1.000 -0.241 core.scoring.hbonds.HBondSet: #B 167 LYS N B 164 ARG O 2.22 148.2 99.2 -95.0 1.000 -0.254 core.scoring.hbonds.HBondSet: #B 168 LEU N B 165 GLN O 2.06 156.0 105.9 -96.2 1.000 -0.731 core.scoring.hbonds.HBondSet: #B 165 GLN NE2B 169 ARG O 2.02 154.2 163.2 -90.6 0.600 -0.731 core.scoring.hbonds.HBondSet: #C 2 THR N C 50 THR O 1.72 154.1 148.6 160.0 1.000 -0.980 core.scoring.hbonds.HBondSet: #C 52 LEU N C 2 THR O 1.55 161.2 156.3 126.4 1.000 -0.001 core.scoring.hbonds.HBondSet: #C 4 TYR OH C 49 GLU OE1 1.43 137.8 91.5 160.8 0.859 -0.322 core.scoring.hbonds.HBondSet: #C 4 TYR N C 52 LEU O 2.12 158.0 146.8 110.8 1.000 -0.956 core.scoring.hbonds.HBondSet: #C 54 ASP N C 4 TYR O 2.02 153.2 152.3 86.2 1.000 -0.814 core.scoring.hbonds.HBondSet: #C 5 LYS N C 76 GLU OE1 1.63 176.7 141.4 -69.2 0.718 -1.026 core.scoring.hbonds.HBondSet: #C 76 GLU N C 5 LYS O 1.69 153.2 142.2 -29.9 1.000 -0.922 core.scoring.hbonds.HBondSet: #C 77 GLY N C 5 LYS O 2.17 159.7 146.5 136.1 1.000 -1.218 core.scoring.hbonds.HBondSet: #C 6 LEU N C 54 ASP O 2.32 137.6 138.1 85.2 1.000 -0.152 core.scoring.hbonds.HBondSet: #C 56 LEU N C 6 LEU O 1.75 173.5 163.1 -159.7 1.000 -0.981 core.scoring.hbonds.HBondSet: #C 7 VAL N C 77 GLY O 2.04 157.7 156.7 -176.3 1.000 -1.280 core.scoring.hbonds.HBondSet: #C 79 LEU N C 7 VAL O 2.04 161.1 151.4 106.5 1.000 -1.011 core.scoring.hbonds.HBondSet: #C 8 VAL N C 56 LEU O 1.70 168.1 175.5 -29.1 1.000 -0.633 core.scoring.hbonds.HBondSet: #C 58 THR N C 8 VAL O 2.51 149.3 152.2 -34.7 1.000 -0.419 core.scoring.hbonds.HBondSet: #C 81 VAL N C 9 VAL O 1.97 169.4 138.7 -95.1 1.000 -1.087 core.scoring.hbonds.HBondSet: #C 9 VAL N C 79 LEU O 1.99 163.0 158.5 69.8 1.000 -1.041 core.scoring.hbonds.HBondSet: #C 14 VAL N C 11 ALA O 2.53 152.2 138.8 -142.7 1.000 -0.663 core.scoring.hbonds.HBondSet: #C 116 ASN ND2C 14 VAL O 1.82 167.4 146.4 -179.9 1.000 -1.537 core.scoring.hbonds.HBondSet: #C 20 THR N C 16 LYS O 1.99 167.4 144.5 -123.1 1.000 -1.282 core.scoring.hbonds.HBondSet: #C 21 ILE N C 17 SER O 1.82 165.5 158.8 -113.3 1.000 -0.929 core.scoring.hbonds.HBondSet: #C 22 GLN N C 18 ALA O 2.38 136.0 129.7 -113.7 1.000 -0.171 core.scoring.hbonds.HBondSet: #C 23 LEU N C 19 LEU O 2.36 161.8 147.0 -120.0 1.000 -0.796 core.scoring.hbonds.HBondSet: #C 24 ILE N C 20 THR O 2.00 166.6 151.1 -111.1 1.000 -1.125 core.scoring.hbonds.HBondSet: #C 25 GLN N C 21 ILE O 1.72 154.7 129.3 -67.1 1.000 -0.607 core.scoring.hbonds.HBondSet: #C 26 ASN N C 21 ILE O 2.57 119.1 135.6 -156.2 1.000 -0.015 core.scoring.hbonds.HBondSet: #C 26 ASN N C 22 GLN O 1.79 133.4 103.5 -60.3 1.000 -0.147 core.scoring.hbonds.HBondSet: #C 22 GLN NE2C 146 ALA O 1.63 154.0 167.5 -163.7 1.000 -0.645 core.scoring.hbonds.HBondSet: #C 149 ARG NE C 22 GLN O 2.21 140.1 113.0 69.0 0.812 -0.272 core.scoring.hbonds.HBondSet: #C 149 ARG NH2C 22 GLN O 1.88 151.2 126.3 147.7 0.812 -1.210 core.scoring.hbonds.HBondSet: #C 42 LYS NZ C 23 LEU O 1.67 132.9 144.5 165.1 0.812 -0.372 core.scoring.hbonds.HBondSet: #C 27 HIS NE2C 25 GLN OE1 1.52 162.8 154.3 6.2 0.435 -1.662 core.scoring.hbonds.HBondSet: #C 38 ASP N C 57 ASP O 2.03 155.3 145.6 -28.1 1.000 -1.404 core.scoring.hbonds.HBondSet: #C 57 ASP N C 38 ASP O 1.79 175.4 159.9 -62.4 1.000 -0.987 core.scoring.hbonds.HBondSet: #C 41 ARG NE C 40 TYR O 1.84 155.4 116.2 116.0 0.671 -0.817 core.scoring.hbonds.HBondSet: #C 40 TYR N C 55 ILE O 2.07 139.9 138.2 60.9 1.000 -0.682 core.scoring.hbonds.HBondSet: #C 55 ILE N C 40 TYR O 2.01 140.2 128.7 -92.3 1.000 -0.492 core.scoring.hbonds.HBondSet: #C 42 LYS N C 53 LEU O 1.92 154.7 134.6 29.2 1.000 -1.568 core.scoring.hbonds.HBondSet: #C 53 LEU N C 42 LYS O 1.68 151.6 151.7 111.2 1.000 -0.308 core.scoring.hbonds.HBondSet: #C 44 VAL N C 51 CYS O 1.85 164.6 152.3 -11.9 1.000 -1.400 core.scoring.hbonds.HBondSet: #C 51 CYS N C 44 VAL O 1.80 154.4 157.7 -123.0 1.000 -0.742 core.scoring.hbonds.HBondSet: #C 46 ILE N C 49 GLU O 1.67 145.0 151.1 -29.9 1.000 -0.420 core.scoring.hbonds.HBondSet: #C 161 ARG NE C 47 ASP OD2 1.79 167.7 111.2 -154.9 0.741 -1.399 core.scoring.hbonds.HBondSet: #C 161 ARG NH2C 47 ASP OD1 1.31 152.2 114.3 134.3 0.741 -0.155 core.scoring.hbonds.HBondSet: #C 164 ARG NH1C 47 ASP OD2 1.79 144.3 119.0 -34.0 0.694 -1.005 core.scoring.hbonds.HBondSet: #C 164 ARG NE C 49 GLU OE1 2.09 148.3 123.1 -106.5 0.765 -0.680 core.scoring.hbonds.HBondSet: #C 164 ARG NH2C 49 GLU OE1 1.98 150.7 130.9 -21.0 0.765 -1.389 core.scoring.hbonds.HBondSet: #C 64 TYR N C 61 GLN O 2.09 163.3 134.6 -104.2 1.000 -1.046 core.scoring.hbonds.HBondSet: #C 67 MET N C 64 TYR O 2.24 163.1 120.2 -110.8 1.000 -0.992 core.scoring.hbonds.HBondSet: #C 68 ARG N C 65 SER O 2.45 162.1 114.3 -110.9 1.000 -0.588 core.scoring.hbonds.HBondSet: #C 71 TYR N C 67 MET O 2.78 160.9 130.8 -139.3 1.000 -0.124 core.scoring.hbonds.HBondSet: #C 72 MET N C 68 ARG O 1.90 156.3 161.6 -113.6 1.000 -0.867 core.scoring.hbonds.HBondSet: #C 68 ARG NH1C 99 GLN OE1 2.34 152.0 138.5 126.6 0.718 -0.553 core.scoring.hbonds.HBondSet: #C 73 ARG N C 69 ASP O 2.24 126.8 126.8 -125.2 1.000 -0.354 core.scoring.hbonds.HBondSet: #C 74 THR N C 70 GLN O 2.31 145.5 139.3 -134.5 1.000 -0.795 core.scoring.hbonds.HBondSet: #C 75 GLY N C 71 TYR O 2.01 145.7 143.8 -113.0 1.000 -0.744 core.scoring.hbonds.HBondSet: #C 78 PHE N C 110 PRO O 1.89 171.1 154.0 -133.0 1.000 -1.258 core.scoring.hbonds.HBondSet: #C 112 VAL N C 78 PHE O 2.26 137.9 153.6 -177.7 1.000 -0.706 core.scoring.hbonds.HBondSet: #C 114 VAL N C 80 CYS O 1.86 155.0 164.5 88.3 1.000 -0.760 core.scoring.hbonds.HBondSet: #C 80 CYS N C 112 VAL O 1.88 162.1 169.5 2.0 1.000 -1.001 core.scoring.hbonds.HBondSet: #C 82 PHE N C 114 VAL O 1.97 151.0 151.7 -114.5 1.000 -0.844 core.scoring.hbonds.HBondSet: #C 116 ASN N C 82 PHE O 1.73 153.8 170.9 -52.7 1.000 -0.479 core.scoring.hbonds.HBondSet: #C 86 ASN N C 83 ALA O 2.10 150.9 123.3 -107.8 1.000 -0.837 core.scoring.hbonds.HBondSet: #C 83 ALA N C 89 SER OG 2.04 170.4 133.9 145.8 1.000 -2.012 core.scoring.hbonds.HBondSet: #C 84 ILE N C 116 ASN O 1.95 159.3 172.6 -73.4 1.000 -0.931 core.scoring.hbonds.HBondSet: #C 124 THR N C 84 ILE O 1.76 153.0 166.8 -131.8 1.000 -0.587 core.scoring.hbonds.HBondSet: #C 125 VAL N C 84 ILE O 2.53 164.3 138.7 -65.9 1.000 -0.489 core.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN O 2.24 126.7 121.2 -94.4 1.000 -0.018 core.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN OD1 2.15 151.2 132.2 -37.0 0.976 -1.308 core.scoring.hbonds.HBondSet: #C 90 PHE N C 86 ASN O 2.49 148.3 136.9 172.5 1.000 -1.021 core.scoring.hbonds.HBondSet: #C 91 GLU N C 87 THR O 1.73 168.1 160.6 -136.9 1.000 -0.842 core.scoring.hbonds.HBondSet: #C 92 ASP N C 88 LYS O 1.77 142.1 145.1 -143.0 1.000 -0.721 core.scoring.hbonds.HBondSet: #C 93 ILE N C 89 SER O 2.27 134.8 151.0 -133.2 1.000 -0.401 core.scoring.hbonds.HBondSet: #C 95 GLN N C 92 ASP O 2.18 123.3 117.3 -80.6 1.000 -0.020 core.scoring.hbonds.HBondSet: #C 96 TYR N C 92 ASP O 2.15 160.9 154.3 168.7 1.000 -1.329 core.scoring.hbonds.HBondSet: #C 97 ARG N C 93 ILE O 1.67 175.6 168.1 -141.3 1.000 -0.605 core.scoring.hbonds.HBondSet: #C 98 GLU N C 94 HIS O 2.15 153.5 139.2 -126.1 1.000 -1.058 core.scoring.hbonds.HBondSet: #C 99 GLN N C 95 GLN O 2.33 146.1 145.4 -117.0 1.000 -0.482 core.scoring.hbonds.HBondSet: #C 100 ILE N C 96 TYR O 2.09 167.1 158.5 -150.8 1.000 -1.289 core.scoring.hbonds.HBondSet: #C 101 LYS N C 97 ARG O 2.11 163.6 148.7 -126.8 1.000 -1.199 core.scoring.hbonds.HBondSet: #C 102 ARG N C 98 GLU O 2.14 156.4 133.1 -120.4 1.000 -1.083 core.scoring.hbonds.HBondSet: #C 103 VAL N C 99 GLN O 1.77 170.6 155.8 -107.8 1.000 -0.867 core.scoring.hbonds.HBondSet: #C 104 LYS N C 100 ILE O 1.74 161.0 159.6 -109.4 1.000 -0.667 core.scoring.hbonds.HBondSet: #C 106 SER N C 101 LYS O 2.41 142.0 129.0 1.7 1.000 -1.169 core.scoring.hbonds.HBondSet: #C 102 ARG NH2C 105 ASP OD1 2.37 145.4 152.0 -158.6 0.318 -0.641 core.scoring.hbonds.HBondSet: #C 108 ASP N C 106 SER OG 2.22 135.0 142.4 -10.1 0.482 -0.020 core.scoring.hbonds.HBondSet: #C 169 ARG NH1C 108 ASP OD2 1.70 129.9 173.3 -0.5 0.412 -0.001 core.scoring.hbonds.HBondSet: #C 142 ILE N C 113 LEU O 1.88 166.1 166.9 171.9 1.000 -1.104 core.scoring.hbonds.HBondSet: #C 113 LEU N C 140 PRO O 1.93 164.7 144.6 -108.0 1.000 -1.073 core.scoring.hbonds.HBondSet: #C 115 GLY N C 142 ILE O 2.04 164.1 154.8 175.7 1.000 -1.446 core.scoring.hbonds.HBondSet: #C 144 THR N C 115 GLY O 2.02 173.4 137.2 103.8 1.000 -1.173 core.scoring.hbonds.HBondSet: #C 120 LEU N C 117 LYS O 1.80 177.0 133.7 -108.6 1.000 -1.051 core.scoring.hbonds.HBondSet: #C 118 CYS N C 144 THR O 1.85 163.3 151.8 126.7 1.000 -1.091 core.scoring.hbonds.HBondSet: #C 123 ARG NH1C 143 GLU OE1 2.17 169.7 110.4 151.0 0.765 -1.461 core.scoring.hbonds.HBondSet: #C 123 ARG NH2C 143 GLU OE2 1.91 161.0 121.8 -138.6 0.765 -1.288 core.scoring.hbonds.HBondSet: #C 123 ARG NE C 125 VAL O 2.03 131.2 124.9 118.0 0.718 -0.374 core.scoring.hbonds.HBondSet: #C 123 ARG NH2C 125 VAL O 1.68 140.4 134.2 -140.9 0.718 -0.735 core.scoring.hbonds.HBondSet: #C 130 ALA N C 126 GLU O 2.53 165.6 156.0 -159.6 1.000 -0.707 core.scoring.hbonds.HBondSet: #C 131 GLN N C 127 SER O 1.87 164.3 151.0 -110.2 1.000 -1.010 core.scoring.hbonds.HBondSet: #C 132 ASP N C 128 ARG O 2.01 146.5 132.7 -107.0 1.000 -0.738 core.scoring.hbonds.HBondSet: #C 133 LEU N C 129 GLN O 1.98 143.1 129.4 -112.3 1.000 -0.717 core.scoring.hbonds.HBondSet: #C 134 ALA N C 130 ALA O 1.82 166.4 162.3 -156.9 1.000 -1.089 core.scoring.hbonds.HBondSet: #C 135 ARG N C 131 GLN O 2.10 173.9 148.9 -111.9 1.000 -1.178 core.scoring.hbonds.HBondSet: #C 135 ARG NH1C 132 ASP OD1 2.38 136.5 145.6 -62.9 0.647 -0.181 core.scoring.hbonds.HBondSet: #C 136 SER N C 132 ASP O 2.12 152.8 137.7 -125.8 1.000 -1.072 core.scoring.hbonds.HBondSet: #C 137 TYR N C 133 LEU O 1.85 167.1 151.6 -134.6 1.000 -1.205 core.scoring.hbonds.HBondSet: #C 139 ILE N C 134 ALA O 1.96 155.3 118.9 78.3 1.000 -0.895 core.scoring.hbonds.HBondSet: #C 141 TYR N D 43 GLN OE1 2.04 144.7 105.1 -161.4 0.882 -1.464 core.scoring.hbonds.HBondSet: #D 43 GLN NE2C 141 TYR O 2.03 157.6 130.4 65.6 0.882 -0.956 core.scoring.hbonds.HBondSet: #C 141 TYR OH C 143 GLU OE2 1.55 152.8 103.6 -1.4 0.929 -1.224 core.scoring.hbonds.HBondSet: #C 148 THR N C 145 SER OG 2.52 155.7 104.8 -76.2 0.718 -0.373 core.scoring.hbonds.HBondSet: #C 145 SER N C 150 GLN O 2.05 141.0 168.7 41.9 1.000 -0.559 core.scoring.hbonds.HBondSet: #C 152 VAL N C 149 ARG O 2.51 168.9 127.3 -107.7 1.000 -0.552 core.scoring.hbonds.HBondSet: #C 149 ARG NH1C 153 GLU OE2 1.56 159.7 126.3 71.8 0.600 -0.384 core.scoring.hbonds.HBondSet: #C 149 ARG NH2C 153 GLU OE2 2.54 125.7 139.4 -17.5 0.600 -0.123 core.scoring.hbonds.HBondSet: #C 155 ALA N C 151 GLY O 1.78 146.1 133.1 -129.0 1.000 -0.800 core.scoring.hbonds.HBondSet: #C 156 PHE N C 152 VAL O 1.89 154.0 157.7 -140.7 1.000 -0.980 core.scoring.hbonds.HBondSet: #C 157 TYR N C 153 GLU O 1.84 163.0 153.4 -86.5 1.000 -0.888 core.scoring.hbonds.HBondSet: #C 158 THR N C 154 ASP O 1.94 154.1 142.2 -89.4 1.000 -0.813 core.scoring.hbonds.HBondSet: #C 159 LEU N C 155 ALA O 2.54 144.2 134.9 -128.1 1.000 -0.262 core.scoring.hbonds.HBondSet: #C 160 VAL N C 156 PHE O 2.21 149.1 137.4 -143.0 1.000 -1.172 core.scoring.hbonds.HBondSet: #C 161 ARG N C 157 TYR O 1.89 162.8 155.6 -160.3 1.000 -1.302 core.scoring.hbonds.HBondSet: #C 162 GLU N C 158 THR O 1.95 165.7 151.2 -131.2 1.000 -1.263 core.scoring.hbonds.HBondSet: #C 163 ILE N C 159 LEU O 2.23 149.1 141.0 -119.3 1.000 -0.761 core.scoring.hbonds.HBondSet: #C 164 ARG N C 160 VAL O 1.88 171.9 160.2 -115.2 1.000 -1.091 core.scoring.hbonds.HBondSet: #C 165 GLN N C 161 ARG O 1.82 176.3 172.4 -139.7 1.000 -0.999 core.scoring.hbonds.HBondSet: #D 1 MET N C 162 GLU OE1 1.82 144.1 91.7 156.6 0.976 -0.691 core.scoring.hbonds.HBondSet: #C 166 HIS N C 162 GLU O 1.92 156.4 138.7 -120.0 1.000 -1.074 core.scoring.hbonds.HBondSet: #C 167 LYS N C 163 ILE O 2.12 124.3 130.8 -138.7 1.000 -0.641 core.scoring.hbonds.HBondSet: #C 168 LEU N C 164 ARG O 1.86 161.1 155.6 -106.6 1.000 -0.912 core.scoring.hbonds.HBondSet: #C 169 ARG N C 165 GLN O 2.29 139.6 150.6 -146.4 1.000 -0.622 core.scoring.hbonds.HBondSet: #D 1 MET N C 165 GLN OE1 2.12 146.2 99.8 128.5 0.835 -0.554 core.scoring.hbonds.HBondSet: #C 171 LEU N C 168 LEU O 1.81 154.8 164.8 -70.6 1.000 -0.694 core.scoring.hbonds.HBondSet: #C 170 LYS NZ C 169 ARG O 1.86 133.9 108.9 117.0 0.224 -0.059 core.scoring.hbonds.HBondSet: #D 2 THR N D 50 THR O 1.98 153.0 167.9 155.1 1.000 -0.894 core.scoring.hbonds.HBondSet: #D 52 LEU N D 2 THR O 1.72 167.6 145.5 124.6 1.000 -0.897 core.scoring.hbonds.HBondSet: #D 4 TYR OH D 49 GLU OE1 1.87 148.2 90.6 -158.3 0.882 -0.520 core.scoring.hbonds.HBondSet: #D 4 TYR N D 52 LEU O 1.66 165.8 167.6 97.1 1.000 -0.435 core.scoring.hbonds.HBondSet: #D 54 ASP N D 4 TYR O 1.72 166.4 154.7 93.8 1.000 -0.648 core.scoring.hbonds.HBondSet: #D 164 ARG NE D 4 TYR OH 2.59 162.8 134.0 74.5 0.882 -0.402 core.scoring.hbonds.HBondSet: #D 77 GLY N D 5 LYS O 2.52 134.7 154.4 -178.2 1.000 -0.113 core.scoring.hbonds.HBondSet: #D 5 LYS N D 76 GLU OE1 1.54 165.0 142.6 22.7 0.765 -1.391 core.scoring.hbonds.HBondSet: #D 76 GLU N D 5 LYS O 1.91 160.2 145.4 -56.2 1.000 -1.136 core.scoring.hbonds.HBondSet: #D 56 LEU N D 6 LEU O 1.72 178.1 168.9 -117.8 1.000 -0.751 core.scoring.hbonds.HBondSet: #D 6 LEU N D 54 ASP O 1.90 160.8 152.3 94.5 1.000 -0.918 core.scoring.hbonds.HBondSet: #D 7 VAL N D 77 GLY O 2.11 157.8 159.9 -165.5 1.000 -1.145 core.scoring.hbonds.HBondSet: #D 79 LEU N D 7 VAL O 1.88 166.4 146.8 124.1 1.000 -1.199 core.scoring.hbonds.HBondSet: #D 8 VAL N D 56 LEU O 1.77 169.6 175.1 81.8 1.000 -0.833 core.scoring.hbonds.HBondSet: #D 58 THR N D 8 VAL O 2.43 152.2 149.9 16.5 1.000 -0.837 core.scoring.hbonds.HBondSet: #D 81 VAL N D 9 VAL O 1.75 169.0 165.2 144.8 1.000 -0.869 core.scoring.hbonds.HBondSet: #D 9 VAL N D 79 LEU O 1.93 170.0 167.2 70.2 1.000 -1.083 core.scoring.hbonds.HBondSet: #D 14 VAL N D 11 ALA O 2.38 148.7 141.4 -128.6 1.000 -0.645 core.scoring.hbonds.HBondSet: #D 116 ASN ND2D 14 VAL O 1.67 147.0 135.1 141.6 1.000 -0.974 core.scoring.hbonds.HBondSet: #D 19 LEU N D 15 GLY O 2.05 151.7 143.9 -99.6 1.000 -0.793 core.scoring.hbonds.HBondSet: #D 20 THR N D 16 LYS O 2.13 166.6 143.6 -107.4 1.000 -1.071 core.scoring.hbonds.HBondSet: #D 17 SER OG D 57 ASP OD2 1.87 114.6 107.7 -177.0 1.000 -0.488 core.scoring.hbonds.HBondSet: #D 21 ILE N D 17 SER O 1.79 154.9 149.8 -137.3 1.000 -0.952 core.scoring.hbonds.HBondSet: #D 22 GLN N D 18 ALA O 1.86 153.5 140.6 -123.6 1.000 -0.977 core.scoring.hbonds.HBondSet: #D 23 LEU N D 19 LEU O 2.14 158.4 150.3 -145.1 1.000 -1.247 core.scoring.hbonds.HBondSet: #D 24 ILE N D 20 THR O 2.07 155.1 140.7 -108.5 1.000 -0.925 core.scoring.hbonds.HBondSet: #D 25 GLN N D 21 ILE O 1.56 132.7 142.6 -9.3 1.000 -0.001 core.scoring.hbonds.HBondSet: #D 26 ASN N D 21 ILE O 2.41 136.2 146.1 167.6 1.000 -0.601 core.scoring.hbonds.HBondSet: #D 149 ARG NE D 22 GLN O 2.12 139.8 117.6 63.3 0.835 -0.464 core.scoring.hbonds.HBondSet: #D 149 ARG NH2D 22 GLN O 2.01 139.9 146.0 137.3 0.835 -0.652 core.scoring.hbonds.HBondSet: #D 29 VAL N D 27 HIS O 2.47 111.1 116.9 -152.8 1.000 -0.086 core.scoring.hbonds.HBondSet: #D 59 ALA N D 37 GLU OE1 2.23 169.0 99.2 -26.6 0.647 -0.979 core.scoring.hbonds.HBondSet: #D 57 ASP N D 38 ASP O 2.02 159.9 148.4 112.1 1.000 -1.038 core.scoring.hbonds.HBondSet: #D 40 TYR N D 55 ILE O 1.66 150.7 149.5 -0.6 1.000 -0.730 core.scoring.hbonds.HBondSet: #D 55 ILE N D 40 TYR O 1.94 155.8 135.9 -80.6 1.000 -0.876 core.scoring.hbonds.HBondSet: #D 41 ARG NH2D 54 ASP OD1 2.11 156.8 122.7 133.7 0.647 -1.186 core.scoring.hbonds.HBondSet: #D 42 LYS N D 53 LEU O 2.24 133.2 129.7 31.0 1.000 -0.930 core.scoring.hbonds.HBondSet: #D 53 LEU N D 42 LYS O 1.82 169.1 144.4 75.9 1.000 -0.975 core.scoring.hbonds.HBondSet: #D 42 LYS NZ D 157 TYR OH 2.05 139.6 157.2 168.5 0.812 -0.099 core.scoring.hbonds.HBondSet: #D 44 VAL N D 51 CYS O 1.90 142.6 139.5 2.6 1.000 -1.373 core.scoring.hbonds.HBondSet: #D 51 CYS N D 44 VAL O 1.71 161.1 161.3 18.3 1.000 -0.780 core.scoring.hbonds.HBondSet: #D 46 ILE N D 49 GLU O 1.90 136.6 145.3 -57.8 1.000 -0.553 core.scoring.hbonds.HBondSet: #D 49 GLU N D 46 ILE O 2.00 157.3 116.2 99.9 1.000 -0.922 core.scoring.hbonds.HBondSet: #D 164 ARG NH2D 46 ILE O 2.07 136.9 109.4 -56.9 0.765 -0.451 core.scoring.hbonds.HBondSet: #D 161 ARG NE D 47 ASP OD2 1.82 167.5 111.8 -159.4 0.718 -1.487 core.scoring.hbonds.HBondSet: #D 161 ARG NH2D 47 ASP OD1 1.72 157.2 113.8 147.4 0.718 -1.127 core.scoring.hbonds.HBondSet: #D 164 ARG NH1D 47 ASP OD2 2.23 122.1 98.1 -39.4 0.647 -0.042 core.scoring.hbonds.HBondSet: #D 164 ARG NE D 49 GLU OE1 2.08 121.5 136.8 -92.4 0.765 -0.014 core.scoring.hbonds.HBondSet: #D 164 ARG NH2D 49 GLU OE1 1.40 140.1 138.2 49.8 0.765 -0.005 core.scoring.hbonds.HBondSet: #D 70 GLN N D 67 MET O 2.17 136.5 115.0 -98.6 1.000 -0.317 core.scoring.hbonds.HBondSet: #D 72 MET N D 68 ARG O 1.99 166.7 160.7 -170.5 1.000 -1.316 core.scoring.hbonds.HBondSet: #D 102 ARG NH1D 69 ASP OD2 2.19 136.9 124.8 139.4 0.459 -0.823 core.scoring.hbonds.HBondSet: #D 73 ARG N D 69 ASP O 1.97 140.8 139.1 -103.9 1.000 -0.550 core.scoring.hbonds.HBondSet: #D 74 THR N D 70 GLN O 2.16 137.2 131.6 -177.7 1.000 -1.376 core.scoring.hbonds.HBondSet: #D 75 GLY N D 72 MET O 2.38 158.1 105.7 -99.7 1.000 -0.419 core.scoring.hbonds.HBondSet: #D 78 PHE N D 110 PRO O 2.05 157.7 144.7 -143.1 1.000 -1.368 core.scoring.hbonds.HBondSet: #D 112 VAL N D 78 PHE O 2.10 143.2 152.5 -172.7 1.000 -1.029 core.scoring.hbonds.HBondSet: #D 114 VAL N D 80 CYS O 1.72 164.9 149.5 117.5 1.000 -0.741 core.scoring.hbonds.HBondSet: #D 80 CYS N D 112 VAL O 1.95 161.0 172.9 34.9 1.000 -0.982 core.scoring.hbonds.HBondSet: #D 82 PHE N D 114 VAL O 2.03 167.4 170.3 75.0 1.000 -1.069 core.scoring.hbonds.HBondSet: #D 116 ASN N D 82 PHE O 2.12 146.4 173.7 -3.8 1.000 -0.636 core.scoring.hbonds.HBondSet: #D 86 ASN N D 83 ALA O 2.54 144.5 114.1 -111.9 1.000 -0.035 core.scoring.hbonds.HBondSet: #D 83 ALA N D 89 SER OG 2.11 146.5 117.3 152.5 0.976 -1.646 core.scoring.hbonds.HBondSet: #D 124 THR N D 84 ILE O 1.93 160.3 139.9 136.2 1.000 -1.379 core.scoring.hbonds.HBondSet: #D 125 VAL N D 84 ILE O 2.05 139.0 162.4 -12.1 1.000 -0.670 core.scoring.hbonds.HBondSet: #D 84 ILE N D 116 ASN O 1.94 147.6 177.3 -97.9 1.000 -0.661 core.scoring.hbonds.HBondSet: #D 89 SER N D 86 ASN OD1 2.00 161.6 108.1 -98.8 0.906 -0.997 core.scoring.hbonds.HBondSet: #D 90 PHE N D 86 ASN O 2.32 158.0 145.2 -158.1 1.000 -1.243 core.scoring.hbonds.HBondSet: #D 91 GLU N D 87 THR O 1.78 158.6 144.7 -139.2 1.000 -1.110 core.scoring.hbonds.HBondSet: #D 88 LYS NZ D 91 GLU OE1 2.12 150.6 156.0 -89.7 0.459 -0.167 core.scoring.hbonds.HBondSet: #D 92 ASP N D 88 LYS O 1.73 149.1 145.6 -122.1 1.000 -0.547 core.scoring.hbonds.HBondSet: #D 93 ILE N D 90 PHE O 2.03 147.4 105.4 -96.7 1.000 -0.527 core.scoring.hbonds.HBondSet: #D 94 HIS N D 91 GLU O 2.28 154.2 119.5 -110.3 1.000 -0.747 core.scoring.hbonds.HBondSet: #D 95 GLN N D 92 ASP O 1.97 143.9 112.2 -97.6 1.000 -0.551 core.scoring.hbonds.HBondSet: #D 96 TYR N D 92 ASP O 2.30 161.1 156.2 175.1 1.000 -1.118 core.scoring.hbonds.HBondSet: #D 97 ARG N D 93 ILE O 2.05 176.1 164.5 -98.8 1.000 -1.133 core.scoring.hbonds.HBondSet: #D 98 GLU N D 94 HIS O 2.48 142.6 122.3 -120.3 1.000 -0.261 core.scoring.hbonds.HBondSet: #D 99 GLN N D 95 GLN O 1.99 161.3 153.0 -125.4 1.000 -1.136 core.scoring.hbonds.HBondSet: #D 100 ILE N D 96 TYR O 1.87 177.4 169.1 -152.0 1.000 -1.131 core.scoring.hbonds.HBondSet: #D 101 LYS N D 97 ARG O 1.86 167.3 142.3 -115.0 1.000 -1.108 core.scoring.hbonds.HBondSet: #D 102 ARG N D 98 GLU O 2.22 125.0 130.7 -126.1 1.000 -0.337 core.scoring.hbonds.HBondSet: #D 102 ARG N D 99 GLN O 2.09 133.2 99.1 -93.1 1.000 -0.018 core.scoring.hbonds.HBondSet: #D 103 VAL N D 99 GLN O 1.88 169.2 172.6 -128.9 1.000 -1.037 core.scoring.hbonds.HBondSet: #D 104 LYS N D 100 ILE O 1.81 170.9 160.9 -48.5 1.000 -1.038 core.scoring.hbonds.HBondSet: #D 106 SER N D 101 LYS O 2.55 140.0 125.9 -41.0 1.000 -0.377 core.scoring.hbonds.HBondSet: #D 108 ASP N D 106 SER OG 2.21 137.3 143.4 13.5 0.459 -0.092 core.scoring.hbonds.HBondSet: #D 142 ILE N D 113 LEU O 2.18 165.5 165.0 143.8 1.000 -1.054 core.scoring.hbonds.HBondSet: #D 113 LEU N D 140 PRO O 1.99 168.8 165.8 -121.5 1.000 -1.121 core.scoring.hbonds.HBondSet: #D 144 THR N D 115 GLY O 2.05 151.3 119.0 102.4 1.000 -0.815 core.scoring.hbonds.HBondSet: #D 115 GLY N D 142 ILE O 2.14 152.6 145.4 126.2 1.000 -0.985 core.scoring.hbonds.HBondSet: #D 117 LYS N D 116 ASN OD1 1.95 135.6 102.0 -56.4 1.000 -0.502 core.scoring.hbonds.HBondSet: #D 146 ALA N D 116 ASN OD1 2.50 148.1 139.3 174.2 1.000 -0.040 core.scoring.hbonds.HBondSet: #D 120 LEU N D 117 LYS O 1.73 153.1 140.1 -82.7 1.000 -0.460 core.scoring.hbonds.HBondSet: #D 117 LYS N D 144 THR O 2.23 116.8 127.4 -123.2 1.000 -0.076 core.scoring.hbonds.HBondSet: #D 118 CYS N D 144 THR O 1.88 157.5 150.5 118.9 1.000 -0.964 core.scoring.hbonds.HBondSet: #D 123 ARG NE D 125 VAL O 1.82 128.0 130.3 143.5 0.624 -0.648 core.scoring.hbonds.HBondSet: #D 130 ALA N D 126 GLU O 2.57 166.7 149.2 -153.7 1.000 -0.741 core.scoring.hbonds.HBondSet: #D 128 ARG NH2D 127 SER OG 2.10 123.3 96.6 53.1 0.412 -0.055 core.scoring.hbonds.HBondSet: #D 131 GLN N D 127 SER O 1.81 150.8 149.5 -138.0 1.000 -0.911 core.scoring.hbonds.HBondSet: #D 132 ASP N D 128 ARG O 1.96 143.7 138.7 -118.4 1.000 -0.770 core.scoring.hbonds.HBondSet: #D 133 LEU N D 129 GLN O 2.05 154.0 149.6 -123.9 1.000 -1.006 core.scoring.hbonds.HBondSet: #D 134 ALA N D 130 ALA O 2.04 172.6 153.4 -117.2 1.000 -1.210 core.scoring.hbonds.HBondSet: #D 135 ARG N D 131 GLN O 2.00 157.8 139.8 -105.8 1.000 -0.974 core.scoring.hbonds.HBondSet: #D 136 SER N D 132 ASP O 1.90 143.1 135.1 -132.5 1.000 -0.952 core.scoring.hbonds.HBondSet: #D 137 TYR N D 133 LEU O 1.93 138.5 144.3 -145.7 1.000 -0.923 core.scoring.hbonds.HBondSet: #D 138 GLY N D 134 ALA O 2.06 114.7 140.4 -145.1 1.000 -0.403 core.scoring.hbonds.HBondSet: #D 139 ILE N D 134 ALA O 1.90 169.0 134.7 69.1 1.000 -1.158 core.scoring.hbonds.HBondSet: #D 138 GLY N D 135 ARG O 2.19 144.5 99.6 -80.6 1.000 -0.216 core.scoring.hbonds.HBondSet: #D 141 TYR OH D 143 GLU OE2 1.45 141.9 141.2 32.0 0.906 -0.834 core.scoring.hbonds.HBondSet: #D 148 THR N D 145 SER OG 2.21 162.4 109.0 -94.6 0.718 -1.869 core.scoring.hbonds.HBondSet: #D 145 SER N D 150 GLN O 2.05 157.8 160.0 -28.2 1.000 -1.124 core.scoring.hbonds.HBondSet: #D 149 ARG N D 145 SER O 2.27 108.0 131.2 -130.5 1.000 0.000 core.scoring.hbonds.HBondSet: #D 150 GLN N D 148 THR OG1 2.01 159.2 116.7 54.1 0.553 -1.978 core.scoring.hbonds.HBondSet: #D 152 VAL N D 149 ARG O 2.08 167.7 133.5 -113.0 1.000 -1.205 core.scoring.hbonds.HBondSet: #D 149 ARG NH1D 153 GLU OE2 1.72 139.9 116.1 110.6 0.624 -0.269 core.scoring.hbonds.HBondSet: #D 149 ARG NH2D 153 GLU OE2 2.14 128.3 171.8 -38.7 0.624 -0.141 core.scoring.hbonds.HBondSet: #D 155 ALA N D 151 GLY O 2.21 144.4 149.7 -122.7 1.000 -0.640 core.scoring.hbonds.HBondSet: #D 156 PHE N D 152 VAL O 2.49 164.9 140.1 -133.1 1.000 -0.831 core.scoring.hbonds.HBondSet: #D 157 TYR N D 153 GLU O 1.61 176.4 168.7 -139.5 1.000 -0.343 core.scoring.hbonds.HBondSet: #D 159 LEU N D 155 ALA O 2.52 140.7 130.8 -124.7 1.000 -0.182 core.scoring.hbonds.HBondSet: #D 160 VAL N D 156 PHE O 2.09 159.7 161.6 -154.7 1.000 -1.128 core.scoring.hbonds.HBondSet: #D 161 ARG N D 157 TYR O 2.63 167.6 136.4 -88.2 1.000 -0.115 core.scoring.hbonds.HBondSet: #D 162 GLU N D 158 THR O 2.14 149.2 143.1 -142.7 1.000 -1.147 core.scoring.hbonds.HBondSet: #D 163 ILE N D 159 LEU O 1.94 160.5 153.2 -126.9 1.000 -1.117 core.scoring.hbonds.HBondSet: #D 164 ARG N D 160 VAL O 1.61 159.8 154.1 -143.4 1.000 -0.367 core.scoring.hbonds.HBondSet: #D 165 GLN N D 161 ARG O 1.72 164.1 141.9 -98.0 1.000 -0.642 core.scoring.hbonds.HBondSet: #D 166 HIS N D 162 GLU O 1.79 161.8 144.1 -107.5 1.000 -0.839 core.scoring.hbonds.HBondSet: #D 167 LYS N D 163 ILE O 1.99 160.5 154.2 -112.8 1.000 -1.029 core.scoring.hbonds.HBondSet: #D 168 LEU N D 165 GLN O 2.12 141.5 110.2 -100.9 1.000 -0.446 core.scoring.hbonds.HBondSet: #D 169 ARG N D 166 HIS O 1.83 168.3 146.2 -120.5 1.000 -1.104 core.scoring.hbonds.HBondSet: #D 170 LYS N D 167 LYS O 2.34 150.5 125.7 -124.0 1.000 -0.782 core.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy core.scoring.hbonds.HBondSet: #A 1 MET N B 162 GLU OE1 1.87 152.3 115.2 157.1 1.000 -1.850 core.scoring.hbonds.HBondSet: #A 1 MET N B 165 GLN OE1 1.59 159.1 136.2 147.7 0.859 -1.567 core.scoring.hbonds.HBondSet: #A 52 LEU N A 2 THR O 1.59 171.0 149.6 134.7 1.000 -0.439 core.scoring.hbonds.HBondSet: #A 2 THR N A 50 THR O 2.01 158.3 155.0 -175.7 1.000 -1.342 core.scoring.hbonds.HBondSet: #A 4 TYR N A 52 LEU O 1.71 146.0 157.4 151.1 1.000 -0.468 core.scoring.hbonds.HBondSet: #A 54 ASP N A 4 TYR O 1.72 151.1 150.2 49.0 1.000 -0.601 core.scoring.hbonds.HBondSet: #A 5 LYS N A 76 GLU OE1 1.52 175.1 149.4 13.9 0.765 -1.324 core.scoring.hbonds.HBondSet: #A 76 GLU N A 5 LYS O 1.97 142.0 123.6 -73.8 1.000 -0.616 core.scoring.hbonds.HBondSet: #A 77 GLY N A 5 LYS O 2.16 141.0 146.4 -155.0 1.000 -0.989 core.scoring.hbonds.HBondSet: #A 6 LEU N A 54 ASP O 1.88 169.2 151.8 102.5 1.000 -1.038 core.scoring.hbonds.HBondSet: #A 56 LEU N A 6 LEU O 2.05 163.6 163.5 167.1 1.000 -1.200 core.scoring.hbonds.HBondSet: #A 7 VAL N A 77 GLY O 1.65 159.9 148.6 -140.0 1.000 -0.669 core.scoring.hbonds.HBondSet: #A 8 VAL N A 56 LEU O 2.14 166.5 145.2 73.7 1.000 -1.058 core.scoring.hbonds.HBondSet: #A 58 THR N A 8 VAL O 2.66 140.8 137.3 32.0 1.000 -0.139 core.scoring.hbonds.HBondSet: #A 81 VAL N A 9 VAL O 1.76 166.8 144.1 -124.3 1.000 -0.996 core.scoring.hbonds.HBondSet: #A 9 VAL N A 79 LEU O 1.98 138.4 151.4 57.5 1.000 -0.592 core.scoring.hbonds.HBondSet: #A 14 VAL N A 11 ALA O 1.88 154.8 146.6 -154.7 1.000 -1.324 core.scoring.hbonds.HBondSet: #A 117 LYS NZ A 13 GLY O 2.09 158.9 168.0 43.3 0.929 -0.307 core.scoring.hbonds.HBondSet: #A 116 ASN ND2A 14 VAL O 2.17 167.3 134.9 147.9 1.000 -1.433 core.scoring.hbonds.HBondSet: #A 19 LEU N A 15 GLY O 1.86 152.2 155.7 -122.2 1.000 -0.811 core.scoring.hbonds.HBondSet: #A 20 THR N A 16 LYS O 1.90 177.7 161.6 -167.9 1.000 -1.327 core.scoring.hbonds.HBondSet: #A 21 ILE N A 17 SER O 1.81 151.9 161.2 83.6 1.000 -0.613 core.scoring.hbonds.HBondSet: #A 17 SER OG A 57 ASP OD2 1.82 126.8 115.0 -166.4 1.000 -0.827 core.scoring.hbonds.HBondSet: #A 22 GLN N A 18 ALA O 2.31 140.8 122.1 -104.6 1.000 -0.323 core.scoring.hbonds.HBondSet: #A 23 LEU N A 19 LEU O 2.28 137.6 137.1 -174.9 1.000 -1.131 core.scoring.hbonds.HBondSet: #A 23 LEU N A 20 THR O 1.97 123.1 112.5 -78.8 1.000 -0.055 core.scoring.hbonds.HBondSet: #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979 core.scoring.hbonds.HBondSet: #A 25 GLN N A 21 ILE O 2.24 105.4 127.6 -17.1 1.000 -0.432 core.scoring.hbonds.HBondSet: #A 149 ARG NH2A 22 GLN O 1.69 156.8 124.3 126.5 0.859 -0.895 core.scoring.hbonds.HBondSet: #A 30 ASP N A 31 GLU OE2 1.95 148.8 110.5 52.5 0.318 -1.124 core.scoring.hbonds.HBondSet: #A 57 ASP N A 38 ASP O 2.02 149.5 176.9 -58.1 1.000 -0.727 core.scoring.hbonds.HBondSet: #A 40 TYR N A 55 ILE O 2.06 133.0 125.1 62.1 1.000 -0.543 core.scoring.hbonds.HBondSet: #A 55 ILE N A 40 TYR O 1.69 157.5 167.5 -58.5 1.000 -0.451 core.scoring.hbonds.HBondSet: #A 42 LYS N A 53 LEU O 2.02 144.4 129.4 31.9 1.000 -1.371 core.scoring.hbonds.HBondSet: #A 53 LEU N A 42 LYS O 1.74 153.8 165.7 -34.7 1.000 -0.598 core.scoring.hbonds.HBondSet: #A 43 GLN NE2B 141 TYR O 1.70 166.6 150.3 33.2 0.859 -1.175 core.scoring.hbonds.HBondSet: #B 141 TYR N A 43 GLN OE1 2.24 131.2 99.3 -167.7 0.859 -0.219 core.scoring.hbonds.HBondSet: #A 44 VAL N A 51 CYS O 1.71 163.4 149.6 -1.3 1.000 -1.165 core.scoring.hbonds.HBondSet: #A 46 ILE N A 49 GLU O 2.07 141.6 134.8 -34.7 1.000 -1.178 core.scoring.hbonds.HBondSet: #A 49 GLU N A 46 ILE O 2.22 146.3 99.6 95.0 1.000 -0.222 core.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD1 2.30 127.4 91.6 172.3 0.718 -0.063 core.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD2 2.37 163.9 86.4 -172.5 0.718 -0.412 core.scoring.hbonds.HBondSet: #A 164 ARG NH1A 47 ASP OD2 1.48 142.3 122.9 -33.8 0.671 -0.468 core.scoring.hbonds.HBondSet: #A 164 ARG NH2A 47 ASP OD2 1.87 128.8 120.1 73.7 0.671 -0.154 core.scoring.hbonds.HBondSet: #B 169 ARG NH1A 49 GLU OE2 1.85 136.1 126.0 132.0 0.624 -0.645 core.scoring.hbonds.HBondSet: #B 169 ARG NH2A 49 GLU OE2 2.28 126.2 161.1 -104.1 0.624 -0.007 core.scoring.hbonds.HBondSet: #A 58 THR N A 56 LEU O 2.50 117.5 111.9 -148.7 1.000 -0.051 core.scoring.hbonds.HBondSet: #A 65 SER N A 63 GLU OE1 1.63 154.5 118.5 115.9 0.224 -0.884 core.scoring.hbonds.HBondSet: #A 68 ARG NH2A 96 TYR OH 1.81 164.5 113.9 -150.2 0.788 -1.692 core.scoring.hbonds.HBondSet: #A 74 THR OG1A 71 TYR O 2.00 159.3 114.5 -39.3 0.576 -0.378 core.scoring.hbonds.HBondSet: #A 71 TYR N A 72 MET O 2.18 108.7 111.7 7.3 1.000 -0.617 core.scoring.hbonds.HBondSet: #A 75 GLY N A 71 TYR O 1.64 137.5 150.1 -159.0 1.000 -0.191 core.scoring.hbonds.HBondSet: #A 104 LYS NZ A 75 GLY O 1.73 151.1 175.2 27.0 0.788 -0.427 core.scoring.hbonds.HBondSet: #A 112 VAL N A 78 PHE O 2.25 148.8 157.4 173.4 1.000 -0.878 core.scoring.hbonds.HBondSet: #A 78 PHE N A 110 PRO O 2.01 158.7 153.2 -144.4 1.000 -1.242 core.scoring.hbonds.HBondSet: #A 80 CYS N A 112 VAL O 2.27 143.1 149.0 68.7 1.000 -0.434 core.scoring.hbonds.HBondSet: #A 114 VAL N A 80 CYS O 2.23 169.9 156.5 101.6 1.000 -0.960 core.scoring.hbonds.HBondSet: #A 116 ASN N A 82 PHE O 1.76 152.5 166.5 -98.5 1.000 -0.518 core.scoring.hbonds.HBondSet: #A 82 PHE N A 114 VAL O 2.14 145.0 155.1 -96.1 1.000 -0.561 core.scoring.hbonds.HBondSet: #A 86 ASN N A 83 ALA O 2.32 149.5 107.5 -109.9 1.000 -0.454 core.scoring.hbonds.HBondSet: #A 83 ALA N A 89 SER OG 1.92 159.9 113.0 146.0 1.000 -2.159 core.scoring.hbonds.HBondSet: #A 84 ILE N A 116 ASN O 2.25 158.9 161.3 -45.4 1.000 -0.878 core.scoring.hbonds.HBondSet: #A 124 THR N A 84 ILE O 1.65 177.5 159.1 166.1 1.000 -0.788 core.scoring.hbonds.HBondSet: #A 88 LYS N A 86 ASN OD1 1.96 146.5 130.0 -97.6 0.600 -0.800 core.scoring.hbonds.HBondSet: #A 90 PHE N A 86 ASN O 2.39 155.4 153.6 -141.6 1.000 -0.744 core.scoring.hbonds.HBondSet: #A 91 GLU N A 87 THR O 2.43 136.5 134.7 -143.4 1.000 -0.557 core.scoring.hbonds.HBondSet: #A 92 ASP N A 88 LYS O 2.28 145.5 141.1 -118.0 1.000 -0.589 core.scoring.hbonds.HBondSet: #A 96 TYR N A 92 ASP O 2.47 148.2 144.3 139.2 1.000 -0.571 core.scoring.hbonds.HBondSet: #A 95 GLN N A 92 ASP O 1.65 147.8 124.5 -102.5 1.000 -0.067 core.scoring.hbonds.HBondSet: #A 97 ARG N A 93 ILE O 2.13 156.0 164.2 -73.0 1.000 -0.838 core.scoring.hbonds.HBondSet: #A 98 GLU N A 94 HIS O 2.17 155.1 127.3 -111.1 1.000 -0.919 core.scoring.hbonds.HBondSet: #A 99 GLN N A 95 GLN O 2.20 147.3 151.5 -140.0 1.000 -0.869 core.scoring.hbonds.HBondSet: #A 100 ILE N A 96 TYR O 2.07 160.1 159.6 177.7 1.000 -1.238 core.scoring.hbonds.HBondSet: #A 101 LYS N A 97 ARG O 2.17 173.1 164.2 -178.2 1.000 -1.217 core.scoring.hbonds.HBondSet: #A 102 ARG N A 98 GLU O 2.38 139.0 138.2 -136.4 1.000 -0.549 core.scoring.hbonds.HBondSet: #A 103 VAL N A 99 GLN O 1.71 166.8 162.3 -144.5 1.000 -0.762 core.scoring.hbonds.HBondSet: #A 104 LYS N A 100 ILE O 1.67 160.9 170.6 -154.6 1.000 -0.436 core.scoring.hbonds.HBondSet: #A 105 ASP N A 102 ARG O 2.25 143.4 93.6 -86.8 1.000 -0.002 core.scoring.hbonds.HBondSet: #A 108 ASP N A 106 SER OG 1.97 152.0 90.6 86.3 0.365 -1.113 core.scoring.hbonds.HBondSet: #A 113 LEU N A 140 PRO O 1.81 148.3 171.8 67.9 1.000 -0.521 core.scoring.hbonds.HBondSet: #A 142 ILE N A 113 LEU O 1.79 150.9 160.0 151.3 1.000 -0.770 core.scoring.hbonds.HBondSet: #A 115 GLY N A 142 ILE O 2.24 157.4 135.9 129.0 1.000 -1.120 core.scoring.hbonds.HBondSet: #A 144 THR N A 115 GLY O 2.13 162.0 119.4 101.2 1.000 -0.987 core.scoring.hbonds.HBondSet: #A 117 LYS N A 116 ASN OD1 1.85 141.7 101.3 -66.8 1.000 -0.539 core.scoring.hbonds.HBondSet: #A 120 LEU N A 117 LYS O 1.95 172.9 143.4 -107.1 1.000 -1.171 core.scoring.hbonds.HBondSet: #A 117 LYS N A 144 THR O 2.01 106.8 129.9 -132.7 1.000 -0.125 core.scoring.hbonds.HBondSet: #A 118 CYS N A 144 THR O 1.90 170.5 123.4 123.6 1.000 -1.398 core.scoring.hbonds.HBondSet: #A 123 ARG NH1A 143 GLU OE2 1.95 158.1 107.0 -145.0 0.741 -1.215 core.scoring.hbonds.HBondSet: #A 123 ARG NH2A 143 GLU OE1 1.63 171.8 119.9 158.6 0.741 -1.303 core.scoring.hbonds.HBondSet: #A 123 ARG NH1A 125 VAL O 2.02 173.1 148.1 -124.0 0.694 -1.007 core.scoring.hbonds.HBondSet: #A 130 ALA N A 126 GLU O 1.87 158.8 152.0 -177.9 1.000 -1.364 core.scoring.hbonds.HBondSet: #A 132 ASP N A 128 ARG O 2.21 150.7 138.4 -109.6 1.000 -0.724 core.scoring.hbonds.HBondSet: #A 133 LEU N A 129 GLN O 2.28 151.1 146.3 -142.0 1.000 -0.960 core.scoring.hbonds.HBondSet: #A 134 ALA N A 130 ALA O 1.79 166.2 162.7 -178.5 1.000 -1.051 core.scoring.hbonds.HBondSet: #A 135 ARG N A 131 GLN O 1.83 166.3 155.5 -99.9 1.000 -0.923 core.scoring.hbonds.HBondSet: #A 136 SER N A 132 ASP O 1.78 156.7 145.2 -115.7 1.000 -0.779 core.scoring.hbonds.HBondSet: #A 137 TYR N A 133 LEU O 1.92 158.6 154.8 -155.1 1.000 -1.247 core.scoring.hbonds.HBondSet: #A 138 GLY N A 134 ALA O 1.83 121.8 139.0 -163.6 1.000 -0.700 core.scoring.hbonds.HBondSet: #A 139 ILE N A 134 ALA O 2.24 163.7 126.8 83.5 1.000 -0.871 core.scoring.hbonds.HBondSet: #A 141 TYR OH A 143 GLU OE2 1.54 139.3 111.7 0.2 0.953 -1.165 core.scoring.hbonds.HBondSet: #A 141 TYR N C 43 GLN OE1 2.08 161.9 118.7 -172.1 0.835 -2.242 core.scoring.hbonds.HBondSet: #C 43 GLN NE2A 141 TYR O 2.33 146.4 124.9 79.1 0.835 -0.190 core.scoring.hbonds.HBondSet: #A 148 THR N A 145 SER OG 2.05 157.6 137.3 -91.6 0.694 -1.629 core.scoring.hbonds.HBondSet: #A 145 SER N A 150 GLN O 2.02 170.9 150.4 -53.6 1.000 -1.299 core.scoring.hbonds.HBondSet: #A 150 GLN N A 148 THR OG1 2.60 158.2 106.0 37.4 0.553 -0.009 core.scoring.hbonds.HBondSet: #A 152 VAL N A 149 ARG O 2.41 170.1 119.9 -103.6 1.000 -0.718 core.scoring.hbonds.HBondSet: #A 149 ARG NH2A 153 GLU OE2 2.57 140.9 135.9 23.0 0.671 -0.460 core.scoring.hbonds.HBondSet: #A 155 ALA N A 151 GLY O 2.17 152.2 149.8 -130.5 1.000 -0.948 core.scoring.hbonds.HBondSet: #A 156 PHE N A 152 VAL O 2.47 167.0 144.2 -123.9 1.000 -0.728 core.scoring.hbonds.HBondSet: #A 157 TYR N A 153 GLU O 1.72 169.3 166.5 -179.4 1.000 -0.834 core.scoring.hbonds.HBondSet: #A 157 TYR OH A 153 GLU OE1 2.17 146.9 99.0 117.3 0.765 -0.012 core.scoring.hbonds.HBondSet: #A 158 THR N A 154 ASP O 1.89 147.3 139.5 -98.2 1.000 -0.633 core.scoring.hbonds.HBondSet: #A 159 LEU N A 155 ALA O 2.17 148.5 137.9 -132.2 1.000 -1.027 core.scoring.hbonds.HBondSet: #A 160 VAL N A 156 PHE O 2.05 159.9 143.0 -132.0 1.000 -1.295 core.scoring.hbonds.HBondSet: #A 161 ARG N A 157 TYR O 1.81 160.4 153.3 -118.9 1.000 -0.892 core.scoring.hbonds.HBondSet: #A 162 GLU N A 158 THR O 2.08 152.2 148.4 -125.7 1.000 -0.984 core.scoring.hbonds.HBondSet: #A 163 ILE N A 159 LEU O 2.04 159.2 154.3 -135.6 1.000 -1.160 core.scoring.hbonds.HBondSet: #A 164 ARG N A 160 VAL O 1.82 170.5 164.7 -100.1 1.000 -0.943 core.scoring.hbonds.HBondSet: #A 165 GLN N A 161 ARG O 1.77 162.3 145.7 -126.0 1.000 -0.962 core.scoring.hbonds.HBondSet: #C 1 MET N A 162 GLU OE2 1.52 173.9 111.2 -150.8 0.859 -1.532 core.scoring.hbonds.HBondSet: #A 166 HIS N A 162 GLU O 1.67 153.5 143.8 -117.4 1.000 -0.382 core.scoring.hbonds.HBondSet: #A 167 LYS N A 163 ILE O 1.81 160.2 169.3 -164.8 1.000 -0.852 core.scoring.hbonds.HBondSet: #C 1 MET N A 165 GLN OE1 1.68 168.3 116.6 -140.8 0.694 -1.841 core.scoring.hbonds.HBondSet: #A 168 LEU N A 165 GLN O 2.16 161.1 119.3 -109.5 1.000 -1.021 core.scoring.hbonds.HBondSet: #A 169 ARG N A 167 LYS O 2.09 119.4 111.3 -127.2 1.000 -0.278 core.scoring.hbonds.HBondSet: #A 169 ARG N A 171 LEU O 2.31 134.6 103.8 72.2 1.000 -0.014 core.scoring.hbonds.HBondSet: #B 1 MET N D 162 GLU OE2 1.78 162.3 101.4 -153.1 0.953 -1.514 core.scoring.hbonds.HBondSet: #B 1 MET N D 165 GLN OE1 2.24 168.6 123.5 -111.6 0.741 -0.769 core.scoring.hbonds.HBondSet: #B 52 LEU N B 2 THR O 1.61 169.6 162.9 148.4 1.000 -0.412 core.scoring.hbonds.HBondSet: #B 2 THR N B 50 THR O 2.03 162.9 155.5 -160.6 1.000 -1.366 core.scoring.hbonds.HBondSet: #B 4 TYR N B 52 LEU O 1.80 164.8 167.3 95.8 1.000 -0.828 core.scoring.hbonds.HBondSet: #B 54 ASP N B 4 TYR O 1.94 154.4 155.9 57.8 1.000 -0.931 core.scoring.hbonds.HBondSet: #B 4 TYR OH B 49 GLU OE1 1.84 151.6 105.5 143.8 0.812 -0.974 core.scoring.hbonds.HBondSet: #B 5 LYS N B 76 GLU OE1 1.53 174.9 152.7 -34.8 0.765 -1.099 core.scoring.hbonds.HBondSet: #B 76 GLU N B 5 LYS O 1.69 161.1 146.8 -26.4 1.000 -1.018 core.scoring.hbonds.HBondSet: #B 77 GLY N B 5 LYS O 2.40 143.5 155.6 146.2 1.000 -0.432 core.scoring.hbonds.HBondSet: #B 6 LEU N B 54 ASP O 2.00 144.1 139.4 96.3 1.000 -0.600 core.scoring.hbonds.HBondSet: #B 56 LEU N B 6 LEU O 1.66 162.8 157.9 174.1 1.000 -0.718 core.scoring.hbonds.HBondSet: #B 79 LEU N B 7 VAL O 1.74 157.3 152.8 147.5 1.000 -0.891 core.scoring.hbonds.HBondSet: #B 7 VAL N B 77 GLY O 2.02 174.4 161.6 166.4 1.000 -1.357 core.scoring.hbonds.HBondSet: #B 58 THR N B 8 VAL O 2.72 146.2 149.3 -11.1 1.000 -0.011 core.scoring.hbonds.HBondSet: #B 8 VAL N B 56 LEU O 1.97 177.7 162.1 69.5 1.000 -1.162 core.scoring.hbonds.HBondSet: #B 9 VAL N B 79 LEU O 1.99 152.6 143.2 57.5 1.000 -1.020 core.scoring.hbonds.HBondSet: #B 81 VAL N B 9 VAL O 1.91 177.5 153.5 -123.6 1.000 -1.243 core.scoring.hbonds.HBondSet: #B 14 VAL N B 11 ALA O 2.39 160.5 137.3 -127.2 1.000 -0.898 core.scoring.hbonds.HBondSet: #B 19 LEU N B 15 GLY O 1.91 147.7 148.4 -139.0 1.000 -0.998 core.scoring.hbonds.HBondSet: #B 20 THR N B 16 LYS O 1.82 178.0 165.1 -147.9 1.000 -1.102 core.scoring.hbonds.HBondSet: #B 21 ILE N B 17 SER O 1.94 143.6 134.8 -118.0 1.000 -0.775 core.scoring.hbonds.HBondSet: #B 17 SER OG B 57 ASP OD2 2.05 111.8 116.7 177.1 1.000 -0.366 core.scoring.hbonds.HBondSet: #B 22 GLN N B 18 ALA O 1.97 153.3 145.9 -100.8 1.000 -0.831 core.scoring.hbonds.HBondSet: #B 23 LEU N B 19 LEU O 2.30 169.7 154.3 -159.7 1.000 -1.230 core.scoring.hbonds.HBondSet: #B 24 ILE N B 20 THR O 2.14 171.9 143.2 -132.6 1.000 -1.403 core.scoring.hbonds.HBondSet: #B 25 GLN N B 21 ILE O 1.99 147.2 133.1 -81.7 1.000 -0.687 core.scoring.hbonds.HBondSet: #B 26 ASN N B 21 ILE O 2.58 123.3 138.4 -158.7 1.000 -0.044 core.scoring.hbonds.HBondSet: #B 26 ASN N B 22 GLN O 1.79 133.6 118.3 -62.9 1.000 -0.337 core.scoring.hbonds.HBondSet: #B 38 ASP N B 57 ASP O 1.85 160.4 146.8 -3.4 1.000 -1.515 core.scoring.hbonds.HBondSet: #B 57 ASP N B 38 ASP O 1.89 149.2 160.7 -105.2 1.000 -0.676 core.scoring.hbonds.HBondSet: #B 40 TYR N B 55 ILE O 2.11 143.2 150.5 52.1 1.000 -0.744 core.scoring.hbonds.HBondSet: #B 55 ILE N B 40 TYR O 2.12 137.4 137.0 -91.8 1.000 -0.380 core.scoring.hbonds.HBondSet: #B 42 LYS N B 53 LEU O 1.91 134.3 138.2 49.9 1.000 -0.670 core.scoring.hbonds.HBondSet: #B 44 VAL N B 51 CYS O 1.91 173.0 163.2 -19.0 1.000 -1.262 core.scoring.hbonds.HBondSet: #B 51 CYS N B 44 VAL O 1.70 159.6 163.0 112.3 1.000 -0.521 core.scoring.hbonds.HBondSet: #B 46 ILE N B 49 GLU O 1.89 149.1 141.5 15.9 1.000 -1.413 core.scoring.hbonds.HBondSet: #B 164 ARG NH2B 46 ILE O 1.91 143.8 123.3 -75.0 0.835 -0.513 core.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD2 2.06 128.7 100.1 -167.7 0.718 -0.614 core.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD1 1.97 118.9 114.3 145.6 0.718 -0.498 core.scoring.hbonds.HBondSet: #B 164 ARG NH1B 47 ASP OD2 1.52 144.2 128.2 -31.0 0.741 -0.595 core.scoring.hbonds.HBondSet: #B 164 ARG NE B 49 GLU OE1 2.22 142.9 142.9 -117.5 0.788 -0.542 core.scoring.hbonds.HBondSet: #B 164 ARG NH2B 49 GLU OE1 2.04 151.6 123.3 -27.3 0.788 -1.398 core.scoring.hbonds.HBondSet: #B 63 GLU N B 62 GLU OE2 2.31 142.0 107.1 -34.1 0.341 -0.378 core.scoring.hbonds.HBondSet: #B 68 ARG N B 64 TYR O 2.21 159.0 142.6 -170.1 1.000 -1.568 core.scoring.hbonds.HBondSet: #B 66 ALA N B 68 ARG O 2.47 136.1 106.6 33.2 1.000 -0.418 core.scoring.hbonds.HBondSet: #B 69 ASP N B 67 MET O 1.74 106.9 117.0 -154.2 1.000 -0.195 core.scoring.hbonds.HBondSet: #B 70 GLN N B 67 MET O 1.98 119.6 120.4 -45.6 1.000 -0.524 core.scoring.hbonds.HBondSet: #B 71 TYR N B 67 MET O 2.16 162.9 149.0 67.5 1.000 -1.022 core.scoring.hbonds.HBondSet: #B 73 ARG N B 69 ASP O 2.51 126.5 117.9 -129.1 1.000 -0.007 core.scoring.hbonds.HBondSet: #B 73 ARG NH2B 69 ASP OD1 2.57 139.8 133.2 -39.3 0.459 -0.260 core.scoring.hbonds.HBondSet: #B 74 THR N B 70 GLN O 2.49 146.7 125.7 -106.1 1.000 -0.149 core.scoring.hbonds.HBondSet: #B 75 GLY N B 71 TYR O 1.87 145.5 145.5 -114.3 1.000 -0.663 core.scoring.hbonds.HBondSet: #B 112 VAL N B 78 PHE O 2.16 146.2 176.3 179.0 1.000 -0.584 core.scoring.hbonds.HBondSet: #B 78 PHE N B 110 PRO O 2.04 158.2 134.9 -140.7 1.000 -1.502 core.scoring.hbonds.HBondSet: #B 114 VAL N B 80 CYS O 1.97 165.7 143.0 81.3 1.000 -1.057 core.scoring.hbonds.HBondSet: #B 80 CYS N B 112 VAL O 1.96 160.5 171.4 -82.6 1.000 -0.954 core.scoring.hbonds.HBondSet: #B 116 ASN N B 82 PHE O 2.01 161.1 144.6 -120.6 1.000 -1.162 core.scoring.hbonds.HBondSet: #B 86 ASN N B 83 ALA O 1.81 161.3 117.4 -107.2 1.000 -0.888 core.scoring.hbonds.HBondSet: #B 83 ALA N B 89 SER OG 1.96 171.4 124.8 149.0 1.000 -2.326 core.scoring.hbonds.HBondSet: #B 84 ILE N B 116 ASN O 1.99 170.8 165.9 28.4 1.000 -1.215 core.scoring.hbonds.HBondSet: #B 124 THR N B 84 ILE O 2.25 143.4 147.0 -164.4 1.000 -1.010 core.scoring.hbonds.HBondSet: #B 89 SER N B 86 ASN OD1 1.35 169.0 136.5 -89.4 0.929 -0.473 core.scoring.hbonds.HBondSet: #B 90 PHE N B 86 ASN O 2.39 149.6 128.9 -139.9 1.000 -0.954 core.scoring.hbonds.HBondSet: #B 87 THR OG1B 124 THR OG1 1.94 120.7 134.4 95.7 0.576 -0.105 core.scoring.hbonds.HBondSet: #B 91 GLU N B 87 THR O 1.86 159.4 146.8 -126.5 1.000 -1.080 core.scoring.hbonds.HBondSet: #B 92 ASP N B 88 LYS O 2.02 132.2 148.3 -133.4 1.000 -0.579 core.scoring.hbonds.HBondSet: #B 96 TYR N B 92 ASP O 2.17 155.0 146.9 149.5 1.000 -1.263 core.scoring.hbonds.HBondSet: #B 97 ARG N B 93 ILE O 2.00 161.9 151.3 -100.5 1.000 -1.005 core.scoring.hbonds.HBondSet: #B 98 GLU N B 94 HIS O 2.09 144.5 133.0 -121.8 1.000 -0.859 core.scoring.hbonds.HBondSet: #B 99 GLN N B 95 GLN O 1.75 174.2 171.9 -172.4 1.000 -0.848 core.scoring.hbonds.HBondSet: #B 100 ILE N B 96 TYR O 1.99 154.7 141.5 -129.9 1.000 -1.183 core.scoring.hbonds.HBondSet: #B 97 ARG NH1B 98 GLU OE1 2.08 102.1 136.3 167.3 0.600 -0.281 core.scoring.hbonds.HBondSet: #B 101 LYS N B 97 ARG O 2.20 169.3 146.3 -103.0 1.000 -1.010 core.scoring.hbonds.HBondSet: #B 102 ARG N B 98 GLU O 2.10 155.0 157.1 -125.1 1.000 -0.944 core.scoring.hbonds.HBondSet: #B 103 VAL N B 99 GLN O 2.07 144.8 153.9 -148.4 1.000 -0.924 core.scoring.hbonds.HBondSet: #B 104 LYS N B 101 LYS O 2.32 156.3 98.4 -104.6 1.000 -0.333 core.scoring.hbonds.HBondSet: #B 105 ASP N B 101 LYS O 1.87 114.7 134.2 -113.9 1.000 -0.001 core.scoring.hbonds.HBondSet: #B 106 SER N B 104 LYS O 2.12 146.8 90.6 135.1 1.000 -0.382 core.scoring.hbonds.HBondSet: #B 142 ILE N B 113 LEU O 2.29 151.5 148.5 168.3 1.000 -1.122 core.scoring.hbonds.HBondSet: #B 113 LEU N B 140 PRO O 2.26 166.9 142.6 -106.9 1.000 -0.939 core.scoring.hbonds.HBondSet: #B 115 GLY N B 142 ILE O 1.89 175.4 163.3 115.9 1.000 -1.115 core.scoring.hbonds.HBondSet: #B 144 THR N B 115 GLY O 1.82 166.4 143.8 108.2 1.000 -0.975 core.scoring.hbonds.HBondSet: #B 116 ASN ND2B 144 THR OG1 2.11 151.9 114.3 74.4 1.000 -1.625 core.scoring.hbonds.HBondSet: #B 120 LEU N B 117 LYS O 1.61 160.9 146.4 -148.9 1.000 -0.638 core.scoring.hbonds.HBondSet: #B 118 CYS N B 144 THR O 2.26 149.6 158.9 128.3 1.000 -0.664 core.scoring.hbonds.HBondSet: #B 122 ALA N B 120 LEU O 2.39 118.6 115.2 -135.1 1.000 -0.091 core.scoring.hbonds.HBondSet: #B 123 ARG NE B 125 VAL O 1.27 158.8 151.8 151.1 0.859 -0.468 core.scoring.hbonds.HBondSet: #B 123 ARG NH1B 143 GLU OE1 2.43 152.6 131.2 154.5 0.835 -1.002 core.scoring.hbonds.HBondSet: #B 123 ARG NH2B 143 GLU OE2 2.05 144.9 97.4 -150.9 0.835 -0.765 core.scoring.hbonds.HBondSet: #B 130 ALA N B 126 GLU O 2.05 144.5 148.6 -178.6 1.000 -1.206 core.scoring.hbonds.HBondSet: #B 126 GLU N B 129 GLN OE1 1.82 136.4 92.4 58.0 0.482 -0.121 core.scoring.hbonds.HBondSet: #B 129 GLN N B 126 GLU O 2.06 119.8 113.4 -80.2 1.000 -0.010 core.scoring.hbonds.HBondSet: #B 128 ARG NH2B 127 SER OG 1.74 118.8 110.7 98.3 0.435 -0.082 core.scoring.hbonds.HBondSet: #B 130 ALA N B 127 SER O 1.83 123.3 115.7 -86.8 1.000 -0.001 core.scoring.hbonds.HBondSet: #B 131 GLN N B 127 SER O 1.62 168.0 152.9 134.3 1.000 -0.522 core.scoring.hbonds.HBondSet: #B 132 ASP N B 128 ARG O 1.71 157.8 144.0 -118.8 1.000 -0.662 core.scoring.hbonds.HBondSet: #B 133 LEU N B 129 GLN O 2.33 152.8 121.1 -102.2 1.000 -0.556 core.scoring.hbonds.HBondSet: #B 134 ALA N B 130 ALA O 1.84 166.9 159.5 -175.0 1.000 -1.226 core.scoring.hbonds.HBondSet: #B 135 ARG N B 131 GLN O 1.92 146.8 146.1 -91.4 1.000 -0.623 core.scoring.hbonds.HBondSet: #B 136 SER N B 132 ASP O 2.11 155.5 152.5 -172.9 1.000 -1.320 core.scoring.hbonds.HBondSet: #B 137 TYR N B 133 LEU O 2.17 133.9 144.9 -123.0 1.000 -0.463 core.scoring.hbonds.HBondSet: #B 138 GLY N B 134 ALA O 1.85 135.9 139.4 -133.7 1.000 -0.690 core.scoring.hbonds.HBondSet: #B 139 ILE N B 134 ALA O 1.78 172.1 146.2 58.4 1.000 -1.059 core.scoring.hbonds.HBondSet: #B 141 TYR OH B 143 GLU OE2 1.30 169.7 124.0 -22.7 0.953 -1.194 core.scoring.hbonds.HBondSet: #B 149 ARG N B 145 SER O 1.85 110.9 146.3 -130.1 1.000 -0.001 core.scoring.hbonds.HBondSet: #B 148 THR N B 145 SER OG 2.10 165.0 108.1 -79.1 0.694 -2.084 core.scoring.hbonds.HBondSet: #B 145 SER N B 150 GLN O 1.80 163.2 158.2 -5.1 1.000 -1.148 core.scoring.hbonds.HBondSet: #B 150 GLN N B 148 THR OG1 2.31 163.9 114.4 48.9 0.576 -1.417 core.scoring.hbonds.HBondSet: #B 152 VAL N B 149 ARG O 2.57 162.8 114.6 -116.9 1.000 -0.414 core.scoring.hbonds.HBondSet: #B 155 ALA N B 151 GLY O 1.98 152.5 142.8 -118.1 1.000 -0.965 core.scoring.hbonds.HBondSet: #B 156 PHE N B 152 VAL O 2.52 168.0 149.9 -128.4 1.000 -0.636 core.scoring.hbonds.HBondSet: #B 157 TYR N B 153 GLU O 2.01 159.5 148.4 -101.6 1.000 -0.968 core.scoring.hbonds.HBondSet: #B 158 THR N B 154 ASP O 1.96 151.7 136.5 -81.7 1.000 -0.789 core.scoring.hbonds.HBondSet: #B 159 LEU N B 155 ALA O 2.49 137.7 130.1 -132.6 1.000 -0.327 core.scoring.hbonds.HBondSet: #B 160 VAL N B 156 PHE O 2.28 136.6 138.3 -137.9 1.000 -0.671 core.scoring.hbonds.HBondSet: #B 161 ARG N B 157 TYR O 2.05 160.9 147.4 -145.4 1.000 -1.405 core.scoring.hbonds.HBondSet: #B 162 GLU N B 158 THR O 1.98 142.2 135.1 -129.6 1.000 -0.935 core.scoring.hbonds.HBondSet: #B 163 ILE N B 159 LEU O 2.27 145.9 130.6 -115.9 1.000 -0.628 core.scoring.hbonds.HBondSet: #B 164 ARG N B 160 VAL O 1.87 170.6 168.8 -122.1 1.000 -1.038 core.scoring.hbonds.HBondSet: #B 165 GLN N B 161 ARG O 1.97 158.8 148.5 -96.5 1.000 -0.933 core.scoring.hbonds.HBondSet: #B 166 HIS N B 162 GLU O 2.15 141.4 126.0 -121.4 1.000 -0.756 core.scoring.hbonds.HBondSet: #B 167 LYS N B 163 ILE O 2.28 116.2 139.1 -144.3 1.000 -0.241 core.scoring.hbonds.HBondSet: #B 167 LYS N B 164 ARG O 2.22 148.2 99.2 -95.0 1.000 -0.254 core.scoring.hbonds.HBondSet: #B 168 LEU N B 165 GLN O 2.06 156.0 105.9 -96.2 1.000 -0.731 core.scoring.hbonds.HBondSet: #B 165 GLN NE2B 169 ARG O 2.02 154.2 163.2 -90.6 0.600 -0.731 core.scoring.hbonds.HBondSet: #C 2 THR N C 50 THR O 1.72 154.1 148.6 160.0 1.000 -0.980 core.scoring.hbonds.HBondSet: #C 52 LEU N C 2 THR O 1.55 161.2 156.3 126.4 1.000 -0.001 core.scoring.hbonds.HBondSet: #C 4 TYR OH C 49 GLU OE1 1.43 137.8 91.5 160.8 0.859 -0.322 core.scoring.hbonds.HBondSet: #C 4 TYR N C 52 LEU O 2.12 158.0 146.8 110.8 1.000 -0.956 core.scoring.hbonds.HBondSet: #C 54 ASP N C 4 TYR O 2.02 153.2 152.3 86.2 1.000 -0.814 core.scoring.hbonds.HBondSet: #C 5 LYS N C 76 GLU OE1 1.63 176.7 141.4 -69.2 0.718 -1.026 core.scoring.hbonds.HBondSet: #C 76 GLU N C 5 LYS O 1.69 153.2 142.2 -29.9 1.000 -0.922 core.scoring.hbonds.HBondSet: #C 77 GLY N C 5 LYS O 2.17 159.7 146.5 136.1 1.000 -1.218 core.scoring.hbonds.HBondSet: #C 6 LEU N C 54 ASP O 2.32 137.6 138.1 85.2 1.000 -0.152 core.scoring.hbonds.HBondSet: #C 56 LEU N C 6 LEU O 1.75 173.5 163.1 -159.7 1.000 -0.981 core.scoring.hbonds.HBondSet: #C 7 VAL N C 77 GLY O 2.04 157.7 156.7 -176.3 1.000 -1.280 core.scoring.hbonds.HBondSet: #C 79 LEU N C 7 VAL O 2.04 161.1 151.4 106.5 1.000 -1.011 core.scoring.hbonds.HBondSet: #C 8 VAL N C 56 LEU O 1.70 168.1 175.5 -29.1 1.000 -0.633 core.scoring.hbonds.HBondSet: #C 58 THR N C 8 VAL O 2.51 149.3 152.2 -34.7 1.000 -0.419 core.scoring.hbonds.HBondSet: #C 81 VAL N C 9 VAL O 1.97 169.4 138.7 -95.1 1.000 -1.087 core.scoring.hbonds.HBondSet: #C 9 VAL N C 79 LEU O 1.99 163.0 158.5 69.8 1.000 -1.041 core.scoring.hbonds.HBondSet: #C 14 VAL N C 11 ALA O 2.53 152.2 138.8 -142.7 1.000 -0.663 core.scoring.hbonds.HBondSet: #C 116 ASN ND2C 14 VAL O 1.82 167.4 146.4 -179.9 1.000 -1.537 core.scoring.hbonds.HBondSet: #C 20 THR N C 16 LYS O 1.99 167.4 144.5 -123.1 1.000 -1.282 core.scoring.hbonds.HBondSet: #C 21 ILE N C 17 SER O 1.82 165.5 158.8 -113.3 1.000 -0.929 core.scoring.hbonds.HBondSet: #C 22 GLN N C 18 ALA O 2.38 136.0 129.7 -113.7 1.000 -0.171 core.scoring.hbonds.HBondSet: #C 23 LEU N C 19 LEU O 2.36 161.8 147.0 -120.0 1.000 -0.796 core.scoring.hbonds.HBondSet: #C 24 ILE N C 20 THR O 2.00 166.6 151.1 -111.1 1.000 -1.125 core.scoring.hbonds.HBondSet: #C 25 GLN N C 21 ILE O 1.72 154.7 129.3 -67.1 1.000 -0.607 core.scoring.hbonds.HBondSet: #C 26 ASN N C 21 ILE O 2.57 119.1 135.6 -156.2 1.000 -0.015 core.scoring.hbonds.HBondSet: #C 26 ASN N C 22 GLN O 1.79 133.4 103.5 -60.3 1.000 -0.147 core.scoring.hbonds.HBondSet: #C 22 GLN NE2C 146 ALA O 1.63 154.0 167.5 -163.7 1.000 -0.645 core.scoring.hbonds.HBondSet: #C 149 ARG NE C 22 GLN O 2.21 140.1 113.0 69.0 0.812 -0.272 core.scoring.hbonds.HBondSet: #C 149 ARG NH2C 22 GLN O 1.88 151.2 126.3 147.7 0.812 -1.210 core.scoring.hbonds.HBondSet: #C 42 LYS NZ C 23 LEU O 1.67 132.9 144.5 165.1 0.812 -0.372 core.scoring.hbonds.HBondSet: #C 27 HIS NE2C 25 GLN OE1 1.52 162.8 154.3 6.2 0.435 -1.662 core.scoring.hbonds.HBondSet: #C 38 ASP N C 57 ASP O 2.03 155.3 145.6 -28.1 1.000 -1.404 core.scoring.hbonds.HBondSet: #C 57 ASP N C 38 ASP O 1.79 175.4 159.9 -62.4 1.000 -0.987 core.scoring.hbonds.HBondSet: #C 41 ARG NE C 40 TYR O 1.84 155.4 116.2 116.0 0.671 -0.817 core.scoring.hbonds.HBondSet: #C 40 TYR N C 55 ILE O 2.07 139.9 138.2 60.9 1.000 -0.682 core.scoring.hbonds.HBondSet: #C 55 ILE N C 40 TYR O 2.01 140.2 128.7 -92.3 1.000 -0.492 core.scoring.hbonds.HBondSet: #C 42 LYS N C 53 LEU O 1.92 154.7 134.6 29.2 1.000 -1.568 core.scoring.hbonds.HBondSet: #C 53 LEU N C 42 LYS O 1.68 151.6 151.7 111.2 1.000 -0.308 core.scoring.hbonds.HBondSet: #C 44 VAL N C 51 CYS O 1.85 164.6 152.3 -11.9 1.000 -1.400 core.scoring.hbonds.HBondSet: #C 51 CYS N C 44 VAL O 1.80 154.4 157.7 -123.0 1.000 -0.742 core.scoring.hbonds.HBondSet: #C 46 ILE N C 49 GLU O 1.67 145.0 151.1 -29.9 1.000 -0.420 core.scoring.hbonds.HBondSet: #C 161 ARG NE C 47 ASP OD2 1.79 167.7 111.2 -154.9 0.741 -1.399 core.scoring.hbonds.HBondSet: #C 161 ARG NH2C 47 ASP OD1 1.31 152.2 114.3 134.3 0.741 -0.155 core.scoring.hbonds.HBondSet: #C 164 ARG NH1C 47 ASP OD2 1.79 144.3 119.0 -34.0 0.694 -1.005 core.scoring.hbonds.HBondSet: #C 164 ARG NE C 49 GLU OE1 2.09 148.3 123.1 -106.5 0.765 -0.680 core.scoring.hbonds.HBondSet: #C 164 ARG NH2C 49 GLU OE1 1.98 150.7 130.9 -21.0 0.765 -1.389 core.scoring.hbonds.HBondSet: #C 64 TYR N C 61 GLN O 2.09 163.3 134.6 -104.2 1.000 -1.046 core.scoring.hbonds.HBondSet: #C 67 MET N C 64 TYR O 2.24 163.1 120.2 -110.8 1.000 -0.992 core.scoring.hbonds.HBondSet: #C 68 ARG N C 65 SER O 2.45 162.1 114.3 -110.9 1.000 -0.588 core.scoring.hbonds.HBondSet: #C 71 TYR N C 67 MET O 2.78 160.9 130.8 -139.3 1.000 -0.124 core.scoring.hbonds.HBondSet: #C 72 MET N C 68 ARG O 1.90 156.3 161.6 -113.6 1.000 -0.867 core.scoring.hbonds.HBondSet: #C 68 ARG NH1C 99 GLN OE1 2.34 152.0 138.5 126.6 0.718 -0.553 core.scoring.hbonds.HBondSet: #C 73 ARG N C 69 ASP O 2.24 126.8 126.8 -125.2 1.000 -0.354 core.scoring.hbonds.HBondSet: #C 74 THR N C 70 GLN O 2.31 145.5 139.3 -134.5 1.000 -0.795 core.scoring.hbonds.HBondSet: #C 75 GLY N C 71 TYR O 2.01 145.7 143.8 -113.0 1.000 -0.744 core.scoring.hbonds.HBondSet: #C 78 PHE N C 110 PRO O 1.89 171.1 154.0 -133.0 1.000 -1.258 core.scoring.hbonds.HBondSet: #C 112 VAL N C 78 PHE O 2.26 137.9 153.6 -177.7 1.000 -0.706 core.scoring.hbonds.HBondSet: #C 114 VAL N C 80 CYS O 1.86 155.0 164.5 88.3 1.000 -0.760 core.scoring.hbonds.HBondSet: #C 80 CYS N C 112 VAL O 1.88 162.1 169.5 2.0 1.000 -1.001 core.scoring.hbonds.HBondSet: #C 82 PHE N C 114 VAL O 1.97 151.0 151.7 -114.5 1.000 -0.844 core.scoring.hbonds.HBondSet: #C 116 ASN N C 82 PHE O 1.73 153.8 170.9 -52.7 1.000 -0.479 core.scoring.hbonds.HBondSet: #C 86 ASN N C 83 ALA O 2.10 150.9 123.3 -107.8 1.000 -0.837 core.scoring.hbonds.HBondSet: #C 83 ALA N C 89 SER OG 2.04 170.4 133.9 145.8 1.000 -2.012 core.scoring.hbonds.HBondSet: #C 84 ILE N C 116 ASN O 1.95 159.3 172.6 -73.4 1.000 -0.931 core.scoring.hbonds.HBondSet: #C 124 THR N C 84 ILE O 1.76 153.0 166.8 -131.8 1.000 -0.587 core.scoring.hbonds.HBondSet: #C 125 VAL N C 84 ILE O 2.53 164.3 138.7 -65.9 1.000 -0.489 core.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN O 2.24 126.7 121.2 -94.4 1.000 -0.018 core.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN OD1 2.15 151.2 132.2 -37.0 0.976 -1.308 core.scoring.hbonds.HBondSet: #C 90 PHE N C 86 ASN O 2.49 148.3 136.9 172.5 1.000 -1.021 core.scoring.hbonds.HBondSet: #C 91 GLU N C 87 THR O 1.73 168.1 160.6 -136.9 1.000 -0.842 core.scoring.hbonds.HBondSet: #C 92 ASP N C 88 LYS O 1.77 142.1 145.1 -143.0 1.000 -0.721 core.scoring.hbonds.HBondSet: #C 93 ILE N C 89 SER O 2.27 134.8 151.0 -133.2 1.000 -0.401 core.scoring.hbonds.HBondSet: #C 95 GLN N C 92 ASP O 2.18 123.3 117.3 -80.6 1.000 -0.020 core.scoring.hbonds.HBondSet: #C 96 TYR N C 92 ASP O 2.15 160.9 154.3 168.7 1.000 -1.329 core.scoring.hbonds.HBondSet: #C 97 ARG N C 93 ILE O 1.67 175.6 168.1 -141.3 1.000 -0.605 core.scoring.hbonds.HBondSet: #C 98 GLU N C 94 HIS O 2.15 153.5 139.2 -126.1 1.000 -1.058 core.scoring.hbonds.HBondSet: #C 99 GLN N C 95 GLN O 2.33 146.1 145.4 -117.0 1.000 -0.482 core.scoring.hbonds.HBondSet: #C 100 ILE N C 96 TYR O 2.09 167.1 158.5 -150.8 1.000 -1.289 core.scoring.hbonds.HBondSet: #C 101 LYS N C 97 ARG O 2.11 163.6 148.7 -126.8 1.000 -1.199 core.scoring.hbonds.HBondSet: #C 102 ARG N C 98 GLU O 2.14 156.4 133.1 -120.4 1.000 -1.083 core.scoring.hbonds.HBondSet: #C 103 VAL N C 99 GLN O 1.77 170.6 155.8 -107.8 1.000 -0.867 core.scoring.hbonds.HBondSet: #C 104 LYS N C 100 ILE O 1.74 161.0 159.6 -109.4 1.000 -0.667 core.scoring.hbonds.HBondSet: #C 106 SER N C 101 LYS O 2.41 142.0 129.0 1.7 1.000 -1.169 core.scoring.hbonds.HBondSet: #C 102 ARG NH2C 105 ASP OD1 2.37 145.4 152.0 -158.6 0.318 -0.641 core.scoring.hbonds.HBondSet: #C 108 ASP N C 106 SER OG 2.22 135.0 142.4 -10.1 0.482 -0.020 core.scoring.hbonds.HBondSet: #C 169 ARG NH1C 108 ASP OD2 1.70 129.9 173.3 -0.5 0.412 -0.001 core.scoring.hbonds.HBondSet: #C 142 ILE N C 113 LEU O 1.88 166.1 166.9 171.9 1.000 -1.104 core.scoring.hbonds.HBondSet: #C 113 LEU N C 140 PRO O 1.93 164.7 144.6 -108.0 1.000 -1.073 core.scoring.hbonds.HBondSet: #C 115 GLY N C 142 ILE O 2.04 164.1 154.8 175.7 1.000 -1.446 core.scoring.hbonds.HBondSet: #C 144 THR N C 115 GLY O 2.02 173.4 137.2 103.8 1.000 -1.173 core.scoring.hbonds.HBondSet: #C 120 LEU N C 117 LYS O 1.80 177.0 133.7 -108.6 1.000 -1.051 core.scoring.hbonds.HBondSet: #C 118 CYS N C 144 THR O 1.85 163.3 151.8 126.7 1.000 -1.091 core.scoring.hbonds.HBondSet: #C 123 ARG NH1C 143 GLU OE1 2.17 169.7 110.4 151.0 0.765 -1.461 core.scoring.hbonds.HBondSet: #C 123 ARG NH2C 143 GLU OE2 1.91 161.0 121.8 -138.6 0.765 -1.288 core.scoring.hbonds.HBondSet: #C 123 ARG NE C 125 VAL O 2.03 131.2 124.9 118.0 0.718 -0.374 core.scoring.hbonds.HBondSet: #C 123 ARG NH2C 125 VAL O 1.68 140.4 134.2 -140.9 0.718 -0.735 core.scoring.hbonds.HBondSet: #C 130 ALA N C 126 GLU O 2.53 165.6 156.0 -159.6 1.000 -0.707 core.scoring.hbonds.HBondSet: #C 131 GLN N C 127 SER O 1.87 164.3 151.0 -110.2 1.000 -1.010 core.scoring.hbonds.HBondSet: #C 132 ASP N C 128 ARG O 2.01 146.5 132.7 -107.0 1.000 -0.738 core.scoring.hbonds.HBondSet: #C 133 LEU N C 129 GLN O 1.98 143.1 129.4 -112.3 1.000 -0.717 core.scoring.hbonds.HBondSet: #C 134 ALA N C 130 ALA O 1.82 166.4 162.3 -156.9 1.000 -1.089 core.scoring.hbonds.HBondSet: #C 135 ARG N C 131 GLN O 2.10 173.9 148.9 -111.9 1.000 -1.178 core.scoring.hbonds.HBondSet: #C 135 ARG NH1C 132 ASP OD1 2.38 136.5 145.6 -62.9 0.647 -0.181 core.scoring.hbonds.HBondSet: #C 136 SER N C 132 ASP O 2.12 152.8 137.7 -125.8 1.000 -1.072 core.scoring.hbonds.HBondSet: #C 137 TYR N C 133 LEU O 1.85 167.1 151.6 -134.6 1.000 -1.205 core.scoring.hbonds.HBondSet: #C 139 ILE N C 134 ALA O 1.96 155.3 118.9 78.3 1.000 -0.895 core.scoring.hbonds.HBondSet: #C 141 TYR N D 43 GLN OE1 2.04 144.7 105.1 -161.4 0.882 -1.464 core.scoring.hbonds.HBondSet: #D 43 GLN NE2C 141 TYR O 2.03 157.6 130.4 65.6 0.882 -0.956 core.scoring.hbonds.HBondSet: #C 141 TYR OH C 143 GLU OE2 1.55 152.8 103.6 -1.4 0.929 -1.224 core.scoring.hbonds.HBondSet: #C 148 THR N C 145 SER OG 2.52 155.7 104.8 -76.2 0.718 -0.373 core.scoring.hbonds.HBondSet: #C 145 SER N C 150 GLN O 2.05 141.0 168.7 41.9 1.000 -0.559 core.scoring.hbonds.HBondSet: #C 152 VAL N C 149 ARG O 2.51 168.9 127.3 -107.7 1.000 -0.552 core.scoring.hbonds.HBondSet: #C 149 ARG NH1C 153 GLU OE2 1.56 159.7 126.3 71.8 0.600 -0.384 core.scoring.hbonds.HBondSet: #C 149 ARG NH2C 153 GLU OE2 2.54 125.7 139.4 -17.5 0.600 -0.123 core.scoring.hbonds.HBondSet: #C 155 ALA N C 151 GLY O 1.78 146.1 133.1 -129.0 1.000 -0.800 core.scoring.hbonds.HBondSet: #C 156 PHE N C 152 VAL O 1.89 154.0 157.7 -140.7 1.000 -0.980 core.scoring.hbonds.HBondSet: #C 157 TYR N C 153 GLU O 1.84 163.0 153.4 -86.5 1.000 -0.888 core.scoring.hbonds.HBondSet: #C 158 THR N C 154 ASP O 1.94 154.1 142.2 -89.4 1.000 -0.813 core.scoring.hbonds.HBondSet: #C 159 LEU N C 155 ALA O 2.54 144.2 134.9 -128.1 1.000 -0.262 core.scoring.hbonds.HBondSet: #C 160 VAL N C 156 PHE O 2.21 149.1 137.4 -143.0 1.000 -1.172 core.scoring.hbonds.HBondSet: #C 161 ARG N C 157 TYR O 1.89 162.8 155.6 -160.3 1.000 -1.302 core.scoring.hbonds.HBondSet: #C 162 GLU N C 158 THR O 1.95 165.7 151.2 -131.2 1.000 -1.263 core.scoring.hbonds.HBondSet: #C 163 ILE N C 159 LEU O 2.23 149.1 141.0 -119.3 1.000 -0.761 core.scoring.hbonds.HBondSet: #C 164 ARG N C 160 VAL O 1.88 171.9 160.2 -115.2 1.000 -1.091 core.scoring.hbonds.HBondSet: #C 165 GLN N C 161 ARG O 1.82 176.3 172.4 -139.7 1.000 -0.999 core.scoring.hbonds.HBondSet: #D 1 MET N C 162 GLU OE1 1.82 144.1 91.7 156.6 0.976 -0.691 core.scoring.hbonds.HBondSet: #C 166 HIS N C 162 GLU O 1.92 156.4 138.7 -120.0 1.000 -1.074 core.scoring.hbonds.HBondSet: #C 167 LYS N C 163 ILE O 2.12 124.3 130.8 -138.7 1.000 -0.641 core.scoring.hbonds.HBondSet: #C 168 LEU N C 164 ARG O 1.86 161.1 155.6 -106.6 1.000 -0.912 core.scoring.hbonds.HBondSet: #C 169 ARG N C 165 GLN O 2.29 139.6 150.6 -146.4 1.000 -0.622 core.scoring.hbonds.HBondSet: #D 1 MET N C 165 GLN OE1 2.12 146.2 99.8 128.5 0.835 -0.554 core.scoring.hbonds.HBondSet: #C 171 LEU N C 168 LEU O 1.81 154.8 164.8 -70.6 1.000 -0.694 core.scoring.hbonds.HBondSet: #C 170 LYS NZ C 169 ARG O 1.86 133.9 108.9 117.0 0.224 -0.059 core.scoring.hbonds.HBondSet: #D 2 THR N D 50 THR O 1.98 153.0 167.9 155.1 1.000 -0.894 core.scoring.hbonds.HBondSet: #D 52 LEU N D 2 THR O 1.72 167.6 145.5 124.6 1.000 -0.897 core.scoring.hbonds.HBondSet: #D 4 TYR OH D 49 GLU OE1 1.87 148.2 90.6 -158.3 0.882 -0.520 core.scoring.hbonds.HBondSet: #D 4 TYR N D 52 LEU O 1.66 165.8 167.6 97.1 1.000 -0.435 core.scoring.hbonds.HBondSet: #D 54 ASP N D 4 TYR O 1.72 166.4 154.7 93.8 1.000 -0.648 core.scoring.hbonds.HBondSet: #D 164 ARG NE D 4 TYR OH 2.59 162.8 134.0 74.5 0.882 -0.402 core.scoring.hbonds.HBondSet: #D 77 GLY N D 5 LYS O 2.52 134.7 154.4 -178.2 1.000 -0.113 core.scoring.hbonds.HBondSet: #D 5 LYS N D 76 GLU OE1 1.54 165.0 142.6 22.7 0.765 -1.391 core.scoring.hbonds.HBondSet: #D 76 GLU N D 5 LYS O 1.91 160.2 145.4 -56.2 1.000 -1.136 core.scoring.hbonds.HBondSet: #D 56 LEU N D 6 LEU O 1.72 178.1 168.9 -117.8 1.000 -0.751 core.scoring.hbonds.HBondSet: #D 6 LEU N D 54 ASP O 1.90 160.8 152.3 94.5 1.000 -0.918 core.scoring.hbonds.HBondSet: #D 7 VAL N D 77 GLY O 2.11 157.8 159.9 -165.5 1.000 -1.145 core.scoring.hbonds.HBondSet: #D 79 LEU N D 7 VAL O 1.88 166.4 146.8 124.1 1.000 -1.199 core.scoring.hbonds.HBondSet: #D 8 VAL N D 56 LEU O 1.77 169.6 175.1 81.8 1.000 -0.833 core.scoring.hbonds.HBondSet: #D 58 THR N D 8 VAL O 2.43 152.2 149.9 16.5 1.000 -0.837 core.scoring.hbonds.HBondSet: #D 81 VAL N D 9 VAL O 1.75 169.0 165.2 144.8 1.000 -0.869 core.scoring.hbonds.HBondSet: #D 9 VAL N D 79 LEU O 1.93 170.0 167.2 70.2 1.000 -1.083 core.scoring.hbonds.HBondSet: #D 14 VAL N D 11 ALA O 2.38 148.7 141.4 -128.6 1.000 -0.645 core.scoring.hbonds.HBondSet: #D 116 ASN ND2D 14 VAL O 1.67 147.0 135.1 141.6 1.000 -0.974 core.scoring.hbonds.HBondSet: #D 19 LEU N D 15 GLY O 2.05 151.7 143.9 -99.6 1.000 -0.793 core.scoring.hbonds.HBondSet: #D 20 THR N D 16 LYS O 2.13 166.6 143.6 -107.4 1.000 -1.071 core.scoring.hbonds.HBondSet: #D 17 SER OG D 57 ASP OD2 1.87 114.6 107.7 -177.0 1.000 -0.488 core.scoring.hbonds.HBondSet: #D 21 ILE N D 17 SER O 1.79 154.9 149.8 -137.3 1.000 -0.952 core.scoring.hbonds.HBondSet: #D 22 GLN N D 18 ALA O 1.86 153.5 140.6 -123.6 1.000 -0.977 core.scoring.hbonds.HBondSet: #D 23 LEU N D 19 LEU O 2.14 158.4 150.3 -145.1 1.000 -1.247 core.scoring.hbonds.HBondSet: #D 24 ILE N D 20 THR O 2.07 155.1 140.7 -108.5 1.000 -0.925 core.scoring.hbonds.HBondSet: #D 25 GLN N D 21 ILE O 1.56 132.7 142.6 -9.3 1.000 -0.001 core.scoring.hbonds.HBondSet: #D 26 ASN N D 21 ILE O 2.41 136.2 146.1 167.6 1.000 -0.601 core.scoring.hbonds.HBondSet: #D 149 ARG NE D 22 GLN O 2.12 139.8 117.6 63.3 0.835 -0.464 core.scoring.hbonds.HBondSet: #D 149 ARG NH2D 22 GLN O 2.01 139.9 146.0 137.3 0.835 -0.652 core.scoring.hbonds.HBondSet: #D 29 VAL N D 27 HIS O 2.47 111.1 116.9 -152.8 1.000 -0.086 core.scoring.hbonds.HBondSet: #D 59 ALA N D 37 GLU OE1 2.23 169.0 99.2 -26.6 0.647 -0.979 core.scoring.hbonds.HBondSet: #D 57 ASP N D 38 ASP O 2.02 159.9 148.4 112.1 1.000 -1.038 core.scoring.hbonds.HBondSet: #D 40 TYR N D 55 ILE O 1.66 150.7 149.5 -0.6 1.000 -0.730 core.scoring.hbonds.HBondSet: #D 55 ILE N D 40 TYR O 1.94 155.8 135.9 -80.6 1.000 -0.876 core.scoring.hbonds.HBondSet: #D 41 ARG NH2D 54 ASP OD1 2.11 156.8 122.7 133.7 0.647 -1.186 core.scoring.hbonds.HBondSet: #D 42 LYS N D 53 LEU O 2.24 133.2 129.7 31.0 1.000 -0.930 core.scoring.hbonds.HBondSet: #D 53 LEU N D 42 LYS O 1.82 169.1 144.4 75.9 1.000 -0.975 core.scoring.hbonds.HBondSet: #D 42 LYS NZ D 157 TYR OH 2.05 139.6 157.2 168.5 0.812 -0.099 core.scoring.hbonds.HBondSet: #D 44 VAL N D 51 CYS O 1.90 142.6 139.5 2.6 1.000 -1.373 core.scoring.hbonds.HBondSet: #D 51 CYS N D 44 VAL O 1.71 161.1 161.3 18.3 1.000 -0.780 core.scoring.hbonds.HBondSet: #D 46 ILE N D 49 GLU O 1.90 136.6 145.3 -57.8 1.000 -0.553 core.scoring.hbonds.HBondSet: #D 49 GLU N D 46 ILE O 2.00 157.3 116.2 99.9 1.000 -0.922 core.scoring.hbonds.HBondSet: #D 164 ARG NH2D 46 ILE O 2.07 136.9 109.4 -56.9 0.765 -0.451 core.scoring.hbonds.HBondSet: #D 161 ARG NE D 47 ASP OD2 1.82 167.5 111.8 -159.4 0.718 -1.487 core.scoring.hbonds.HBondSet: #D 161 ARG NH2D 47 ASP OD1 1.72 157.2 113.8 147.4 0.718 -1.127 core.scoring.hbonds.HBondSet: #D 164 ARG NH1D 47 ASP OD2 2.23 122.1 98.1 -39.4 0.647 -0.042 core.scoring.hbonds.HBondSet: #D 164 ARG NE D 49 GLU OE1 2.08 121.5 136.8 -92.4 0.765 -0.014 core.scoring.hbonds.HBondSet: #D 164 ARG NH2D 49 GLU OE1 1.40 140.1 138.2 49.8 0.765 -0.005 core.scoring.hbonds.HBondSet: #D 70 GLN N D 67 MET O 2.17 136.5 115.0 -98.6 1.000 -0.317 core.scoring.hbonds.HBondSet: #D 72 MET N D 68 ARG O 1.99 166.7 160.7 -170.5 1.000 -1.316 core.scoring.hbonds.HBondSet: #D 102 ARG NH1D 69 ASP OD2 2.19 136.9 124.8 139.4 0.459 -0.823 core.scoring.hbonds.HBondSet: #D 73 ARG N D 69 ASP O 1.97 140.8 139.1 -103.9 1.000 -0.550 core.scoring.hbonds.HBondSet: #D 74 THR N D 70 GLN O 2.16 137.2 131.6 -177.7 1.000 -1.376 core.scoring.hbonds.HBondSet: #D 75 GLY N D 72 MET O 2.38 158.1 105.7 -99.7 1.000 -0.419 core.scoring.hbonds.HBondSet: #D 78 PHE N D 110 PRO O 2.05 157.7 144.7 -143.1 1.000 -1.368 core.scoring.hbonds.HBondSet: #D 112 VAL N D 78 PHE O 2.10 143.2 152.5 -172.7 1.000 -1.029 core.scoring.hbonds.HBondSet: #D 114 VAL N D 80 CYS O 1.72 164.9 149.5 117.5 1.000 -0.741 core.scoring.hbonds.HBondSet: #D 80 CYS N D 112 VAL O 1.95 161.0 172.9 34.9 1.000 -0.982 core.scoring.hbonds.HBondSet: #D 82 PHE N D 114 VAL O 2.03 167.4 170.3 75.0 1.000 -1.069 core.scoring.hbonds.HBondSet: #D 116 ASN N D 82 PHE O 2.12 146.4 173.7 -3.8 1.000 -0.636 core.scoring.hbonds.HBondSet: #D 86 ASN N D 83 ALA O 2.54 144.5 114.1 -111.9 1.000 -0.035 core.scoring.hbonds.HBondSet: #D 83 ALA N D 89 SER OG 2.11 146.5 117.3 152.5 0.976 -1.646 core.scoring.hbonds.HBondSet: #D 124 THR N D 84 ILE O 1.93 160.3 139.9 136.2 1.000 -1.379 core.scoring.hbonds.HBondSet: #D 125 VAL N D 84 ILE O 2.05 139.0 162.4 -12.1 1.000 -0.670 core.scoring.hbonds.HBondSet: #D 84 ILE N D 116 ASN O 1.94 147.6 177.3 -97.9 1.000 -0.661 core.scoring.hbonds.HBondSet: #D 89 SER N D 86 ASN OD1 2.00 161.6 108.1 -98.8 0.906 -0.997 core.scoring.hbonds.HBondSet: #D 90 PHE N D 86 ASN O 2.32 158.0 145.2 -158.1 1.000 -1.243 core.scoring.hbonds.HBondSet: #D 91 GLU N D 87 THR O 1.78 158.6 144.7 -139.2 1.000 -1.110 core.scoring.hbonds.HBondSet: #D 88 LYS NZ D 91 GLU OE1 2.12 150.6 156.0 -89.7 0.459 -0.167 core.scoring.hbonds.HBondSet: #D 92 ASP N D 88 LYS O 1.73 149.1 145.6 -122.1 1.000 -0.547 core.scoring.hbonds.HBondSet: #D 93 ILE N D 90 PHE O 2.03 147.4 105.4 -96.7 1.000 -0.527 core.scoring.hbonds.HBondSet: #D 94 HIS N D 91 GLU O 2.28 154.2 119.5 -110.3 1.000 -0.747 core.scoring.hbonds.HBondSet: #D 95 GLN N D 92 ASP O 1.97 143.9 112.2 -97.6 1.000 -0.551 core.scoring.hbonds.HBondSet: #D 96 TYR N D 92 ASP O 2.30 161.1 156.2 175.1 1.000 -1.118 core.scoring.hbonds.HBondSet: #D 97 ARG N D 93 ILE O 2.05 176.1 164.5 -98.8 1.000 -1.133 core.scoring.hbonds.HBondSet: #D 98 GLU N D 94 HIS O 2.48 142.6 122.3 -120.3 1.000 -0.261 core.scoring.hbonds.HBondSet: #D 99 GLN N D 95 GLN O 1.99 161.3 153.0 -125.4 1.000 -1.136 core.scoring.hbonds.HBondSet: #D 100 ILE N D 96 TYR O 1.87 177.4 169.1 -152.0 1.000 -1.131 core.scoring.hbonds.HBondSet: #D 101 LYS N D 97 ARG O 1.86 167.3 142.3 -115.0 1.000 -1.108 core.scoring.hbonds.HBondSet: #D 102 ARG N D 98 GLU O 2.22 125.0 130.7 -126.1 1.000 -0.337 core.scoring.hbonds.HBondSet: #D 102 ARG N D 99 GLN O 2.09 133.2 99.1 -93.1 1.000 -0.018 core.scoring.hbonds.HBondSet: #D 103 VAL N D 99 GLN O 1.88 169.2 172.6 -128.9 1.000 -1.037 core.scoring.hbonds.HBondSet: #D 104 LYS N D 100 ILE O 1.81 170.9 160.9 -48.5 1.000 -1.038 core.scoring.hbonds.HBondSet: #D 106 SER N D 101 LYS O 2.55 140.0 125.9 -41.0 1.000 -0.377 core.scoring.hbonds.HBondSet: #D 108 ASP N D 106 SER OG 2.21 137.3 143.4 13.5 0.459 -0.092 core.scoring.hbonds.HBondSet: #D 142 ILE N D 113 LEU O 2.18 165.5 165.0 143.8 1.000 -1.054 core.scoring.hbonds.HBondSet: #D 113 LEU N D 140 PRO O 1.99 168.8 165.8 -121.5 1.000 -1.121 core.scoring.hbonds.HBondSet: #D 144 THR N D 115 GLY O 2.05 151.3 119.0 102.4 1.000 -0.815 core.scoring.hbonds.HBondSet: #D 115 GLY N D 142 ILE O 2.14 152.6 145.4 126.2 1.000 -0.985 core.scoring.hbonds.HBondSet: #D 117 LYS N D 116 ASN OD1 1.95 135.6 102.0 -56.4 1.000 -0.502 core.scoring.hbonds.HBondSet: #D 146 ALA N D 116 ASN OD1 2.50 148.1 139.3 174.2 1.000 -0.040 core.scoring.hbonds.HBondSet: #D 120 LEU N D 117 LYS O 1.73 153.1 140.1 -82.7 1.000 -0.460 core.scoring.hbonds.HBondSet: #D 117 LYS N D 144 THR O 2.23 116.8 127.4 -123.2 1.000 -0.076 core.scoring.hbonds.HBondSet: #D 118 CYS N D 144 THR O 1.88 157.5 150.5 118.9 1.000 -0.964 core.scoring.hbonds.HBondSet: #D 123 ARG NE D 125 VAL O 1.82 128.0 130.3 143.5 0.624 -0.648 core.scoring.hbonds.HBondSet: #D 130 ALA N D 126 GLU O 2.57 166.7 149.2 -153.7 1.000 -0.741 core.scoring.hbonds.HBondSet: #D 128 ARG NH2D 127 SER OG 2.10 123.3 96.6 53.1 0.412 -0.055 core.scoring.hbonds.HBondSet: #D 131 GLN N D 127 SER O 1.81 150.8 149.5 -138.0 1.000 -0.911 core.scoring.hbonds.HBondSet: #D 132 ASP N D 128 ARG O 1.96 143.7 138.7 -118.4 1.000 -0.770 core.scoring.hbonds.HBondSet: #D 133 LEU N D 129 GLN O 2.05 154.0 149.6 -123.9 1.000 -1.006 core.scoring.hbonds.HBondSet: #D 134 ALA N D 130 ALA O 2.04 172.6 153.4 -117.2 1.000 -1.210 core.scoring.hbonds.HBondSet: #D 135 ARG N D 131 GLN O 2.00 157.8 139.8 -105.8 1.000 -0.974 core.scoring.hbonds.HBondSet: #D 136 SER N D 132 ASP O 1.90 143.1 135.1 -132.5 1.000 -0.952 core.scoring.hbonds.HBondSet: #D 137 TYR N D 133 LEU O 1.93 138.5 144.3 -145.7 1.000 -0.923 core.scoring.hbonds.HBondSet: #D 138 GLY N D 134 ALA O 2.06 114.7 140.4 -145.1 1.000 -0.403 core.scoring.hbonds.HBondSet: #D 139 ILE N D 134 ALA O 1.90 169.0 134.7 69.1 1.000 -1.158 core.scoring.hbonds.HBondSet: #D 138 GLY N D 135 ARG O 2.19 144.5 99.6 -80.6 1.000 -0.216 core.scoring.hbonds.HBondSet: #D 141 TYR OH D 143 GLU OE2 1.45 141.9 141.2 32.0 0.906 -0.834 core.scoring.hbonds.HBondSet: #D 148 THR N D 145 SER OG 2.21 162.4 109.0 -94.6 0.718 -1.869 core.scoring.hbonds.HBondSet: #D 145 SER N D 150 GLN O 2.05 157.8 160.0 -28.2 1.000 -1.124 core.scoring.hbonds.HBondSet: #D 149 ARG N D 145 SER O 2.27 108.0 131.2 -130.5 1.000 0.000 core.scoring.hbonds.HBondSet: #D 150 GLN N D 148 THR OG1 2.01 159.2 116.7 54.1 0.553 -1.978 core.scoring.hbonds.HBondSet: #D 152 VAL N D 149 ARG O 2.08 167.7 133.5 -113.0 1.000 -1.205 core.scoring.hbonds.HBondSet: #D 149 ARG NH1D 153 GLU OE2 1.72 139.9 116.1 110.6 0.624 -0.269 core.scoring.hbonds.HBondSet: #D 149 ARG NH2D 153 GLU OE2 2.14 128.3 171.8 -38.7 0.624 -0.141 core.scoring.hbonds.HBondSet: #D 155 ALA N D 151 GLY O 2.21 144.4 149.7 -122.7 1.000 -0.640 core.scoring.hbonds.HBondSet: #D 156 PHE N D 152 VAL O 2.49 164.9 140.1 -133.1 1.000 -0.831 core.scoring.hbonds.HBondSet: #D 157 TYR N D 153 GLU O 1.61 176.4 168.7 -139.5 1.000 -0.343 core.scoring.hbonds.HBondSet: #D 159 LEU N D 155 ALA O 2.52 140.7 130.8 -124.7 1.000 -0.182 core.scoring.hbonds.HBondSet: #D 160 VAL N D 156 PHE O 2.09 159.7 161.6 -154.7 1.000 -1.128 core.scoring.hbonds.HBondSet: #D 161 ARG N D 157 TYR O 2.63 167.6 136.4 -88.2 1.000 -0.115 core.scoring.hbonds.HBondSet: #D 162 GLU N D 158 THR O 2.14 149.2 143.1 -142.7 1.000 -1.147 core.scoring.hbonds.HBondSet: #D 163 ILE N D 159 LEU O 1.94 160.5 153.2 -126.9 1.000 -1.117 core.scoring.hbonds.HBondSet: #D 164 ARG N D 160 VAL O 1.61 159.8 154.1 -143.4 1.000 -0.367 core.scoring.hbonds.HBondSet: #D 165 GLN N D 161 ARG O 1.72 164.1 141.9 -98.0 1.000 -0.642 core.scoring.hbonds.HBondSet: #D 166 HIS N D 162 GLU O 1.79 161.8 144.1 -107.5 1.000 -0.839 core.scoring.hbonds.HBondSet: #D 167 LYS N D 163 ILE O 1.99 160.5 154.2 -112.8 1.000 -1.029 core.scoring.hbonds.HBondSet: #D 168 LEU N D 165 GLN O 2.12 141.5 110.2 -100.9 1.000 -0.446 core.scoring.hbonds.HBondSet: #D 169 ARG N D 166 HIS O 1.83 168.3 146.2 -120.5 1.000 -1.104 core.scoring.hbonds.HBondSet: #D 170 LYS N D 167 LYS O 2.34 150.5 125.7 -124.0 1.000 -0.782 #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979 ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: false EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: false HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: false HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 3775.511701096452 None 926 407 -1.2098840439684349 0.10835353848860374 1.5729435146961963 core.import_pose.import_pose: File '../test/data/workshops/1YY9.clean.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 2 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 179 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 179 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 179 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 179 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 192 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 192 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 192 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 192 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 193 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 193 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 193 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 193 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 257 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 257 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 257 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 257 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 299 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 299 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 299 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 299 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 299 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 299 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 502 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 502 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 502 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 502 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 502 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 502 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 518 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 518 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 518 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 518 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 520 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 520 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 520 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 520 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 522 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 522 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 522 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 522 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 522 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 522 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 613 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 631 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 631 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 631 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 631 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 631 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 631 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 739 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 739 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 739 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 739 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 801 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 801 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 801 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 801 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG:CtermProteinFull 824 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 959 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 959 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 959 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 959 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 1039 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 1039 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 1039 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 1039 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 1044 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:CtermProteinFull 1044 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 1044 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 1044 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 1044 core.conformation.Conformation: Found disulfide between residues 6 33 core.conformation.Conformation: Found disulfide between residues 132 162 core.conformation.Conformation: Found disulfide between residues 165 174 core.conformation.Conformation: Found disulfide between residues 169 182 core.conformation.Conformation: Found disulfide between residues 190 198 core.conformation.Conformation: Found disulfide between residues 194 206 core.conformation.Conformation: Found disulfide between residues 207 215 core.conformation.Conformation: Found disulfide between residues 211 223 core.conformation.Conformation: Found disulfide between residues 226 235 core.conformation.Conformation: Found disulfide between residues 239 266 core.conformation.Conformation: Found disulfide between residues 270 282 core.conformation.Conformation: Found disulfide between residues 286 301 core.conformation.Conformation: Found disulfide between residues 304 308 core.conformation.Conformation: Found disulfide between residues 312 337 core.conformation.Conformation: Found disulfide between residues 445 474 core.conformation.Conformation: Found disulfide between residues 481 490 core.conformation.Conformation: Found disulfide between residues 485 498 core.conformation.Conformation: Found disulfide between residues 501 510 core.conformation.Conformation: Found disulfide between residues 514 530 core.conformation.Conformation: Found disulfide between residues 533 546 core.conformation.Conformation: Found disulfide between residues 537 554 core.conformation.Conformation: Found disulfide between residues 557 566 core.conformation.Conformation: Found disulfide between residues 570 592 core.conformation.Conformation: Found disulfide between residues 595 603 core.conformation.Conformation: Found disulfide between residues 599 611 core.conformation.Conformation: Found disulfide between residues 636 701 core.conformation.Conformation: Found disulfide between residues 747 807 core.conformation.Conformation: Found disulfide between residues 846 919 core.conformation.Conformation: Found disulfide between residues 970 1026 core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 2 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 138 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 179 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 192 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 193 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 257 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 299 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 502 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 518 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 520 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 522 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 631 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 739 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 801 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 824 because of missing atom number 7 atom name CG core.pack.pack_missing_sidechains: packing residue number 959 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 1039 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 1040 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 1044 because of missing atom number 7 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.pack_rotamers: built 313 rotamers at 23 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph Finished Workshop3test in 0:00:08.378195

mac.clang.python310.PyRosetta.unit.Workshop4test 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Iteration: 0 Score: 1.977790558838489 Low Score: 1.9387244928752159 Iteration: 1 Score: 2.0097867163563627 Low Score: 1.9387244928752159 Iteration: 2 Score: 2.0097867163563627 Low Score: 1.9387244928752159 Iteration: 3 Score: 2.0097867163563627 Low Score: 1.9387244928752159 Iteration: 4 Score: 5.38036979990547 Low Score: 1.9387244928752159 Iteration: 5 Score: 2.0097867163563627 Low Score: 1.9387244928752159 Iteration: 6 Score: 2.0097867163563627 Low Score: 1.9387244928752159 Iteration: 7 Score: 2.0097867163563627 Low Score: 1.9387244928752159 Iteration: 8 Score: 7.64999014975617 Low Score: 1.9387244928752159 Iteration: 9 Score: 2.464876213054378 Low Score: 1.9387244928752159 Iteration: 10 Score: 2.1479826725554947 Low Score: 1.9387244928752159 Iteration: 11 Score: 10.386339561824382 Low Score: 1.9387244928752159 Iteration: 12 Score: 2.1444565451770856 Low Score: 1.9387244928752159 Iteration: 13 Score: 1.4429280667934234 Low Score: 1.9387244928752159 Iteration: 14 Score: 1.4891647329272582 Low Score: 1.4429280667934234 Iteration: 15 Score: 1.5153185319617766 Low Score: 1.4429280667934234 Iteration: 16 Score: 1.5153185319617766 Low Score: 1.4429280667934234 Iteration: 17 Score: 1.5027474011644646 Low Score: 1.4429280667934234 Iteration: 18 Score: 1.5247901196971494 Low Score: 1.4429280667934234 Iteration: 19 Score: 1.5649245236352236 Low Score: 1.4429280667934234 Iteration: 20 Score: 1.596619197236282 Low Score: 1.4429280667934234 Iteration: 21 Score: 1.3448865764237974 Low Score: 1.4429280667934234 Iteration: 22 Score: 5.050425035641338 Low Score: 1.3448865764237974 Iteration: 23 Score: 1.5041534923668873 Low Score: 1.3448865764237974 Iteration: 24 Score: 1.5041534923668873 Low Score: 1.3448865764237974 Iteration: 25 Score: 1.5176060629211534 Low Score: 1.3448865764237974 Iteration: 26 Score: 1.5423351361629942 Low Score: 1.3448865764237974 Iteration: 27 Score: 1.505973378198612 Low Score: 1.3448865764237974 Iteration: 28 Score: 5.227981810191698 Low Score: 1.3448865764237974 Iteration: 29 Score: 1.4993649318738331 Low Score: 1.3448865764237974 Iteration: 30 Score: 0.7962106029569558 Low Score: 1.3448865764237974 Iteration: 31 Score: 3.676543522104674 Low Score: 0.7962106029569558 Iteration: 32 Score: 0.6609701089700559 Low Score: 0.7962106029569558 Iteration: 33 Score: 8.631683368599177 Low Score: 0.6609701089700559 Iteration: 34 Score: 0.6616698375348697 Low Score: 0.6609701089700559 Iteration: 35 Score: 0.6945422945024635 Low Score: 0.6609701089700559 Iteration: 36 Score: 0.6945422945024635 Low Score: 0.6609701089700559 Iteration: 37 Score: 0.05727758461650012 Low Score: 0.6609701089700559 Iteration: 38 Score: 0.1251429758384175 Low Score: 0.05727758461650012 Iteration: 39 Score: -0.5720107269243764 Low Score: 0.05727758461650012 Iteration: 40 Score: -0.6268704204136766 Low Score: -0.5720107269243764 Iteration: 41 Score: -0.5248395521954485 Low Score: -0.6268704204136766 Iteration: 42 Score: 5.017271710795997 Low Score: -0.6268704204136766 Iteration: 43 Score: -0.48023539207575716 Low Score: -0.6268704204136766 Iteration: 44 Score: 0.7575778023691315 Low Score: -0.6268704204136766 Iteration: 45 Score: -0.7034623985614177 Low Score: -0.6268704204136766 Iteration: 46 Score: -0.7290799842462192 Low Score: -0.7034623985614177 Iteration: 47 Score: -0.5480660576928456 Low Score: -0.7290799842462192 Iteration: 48 Score: 0.42485612807666673 Low Score: -0.7290799842462192 Iteration: 49 Score: 0.46117769694045574 Low Score: -0.7290799842462192 Iteration: 50 Score: 0.4069887845941569 Low Score: -0.7290799842462192 Iteration: 51 Score: 0.38845485492458653 Low Score: -0.7290799842462192 Iteration: 52 Score: 0.5298788283694842 Low Score: -0.7290799842462192 Iteration: 53 Score: 0.570957828974568 Low Score: -0.7290799842462192 Iteration: 54 Score: 0.6104545385181384 Low Score: -0.7290799842462192 Iteration: 55 Score: 0.6104545385181384 Low Score: -0.7290799842462192 Iteration: 56 Score: 0.5935399750848482 Low Score: -0.7290799842462192 Iteration: 57 Score: 0.5935399750848482 Low Score: -0.7290799842462192 Iteration: 58 Score: 0.5263235741138503 Low Score: -0.7290799842462192 Iteration: 59 Score: 0.5263235741138503 Low Score: -0.7290799842462192 Iteration: 60 Score: 0.5817690634400279 Low Score: -0.7290799842462192 Iteration: 61 Score: 0.5817690634400279 Low Score: -0.7290799842462192 Iteration: 62 Score: 2.097871251204607 Low Score: -0.7290799842462192 Iteration: 63 Score: 1.5731480223716199 Low Score: -0.7290799842462192 Iteration: 64 Score: 1.5810319003375293 Low Score: -0.7290799842462192 Iteration: 65 Score: 1.5810319003375293 Low Score: -0.7290799842462192 Iteration: 66 Score: 1.3416922286899027 Low Score: -0.7290799842462192 Iteration: 67 Score: 1.2940649978569976 Low Score: -0.7290799842462192 Iteration: 68 Score: 1.2940649978569976 Low Score: -0.7290799842462192 Iteration: 69 Score: 7.390639665226889 Low Score: -0.7290799842462192 Iteration: 70 Score: 6.456994187199169 Low Score: -0.7290799842462192 Iteration: 71 Score: 1.3576969929127412 Low Score: -0.7290799842462192 Iteration: 72 Score: 1.3322668521507977 Low Score: -0.7290799842462192 Iteration: 73 Score: 1.2236386438346836 Low Score: -0.7290799842462192 Iteration: 74 Score: 1.1681068552499436 Low Score: -0.7290799842462192 Iteration: 75 Score: 1.238598181986358 Low Score: -0.7290799842462192 Iteration: 76 Score: 0.6021658337778968 Low Score: -0.7290799842462192 Iteration: 77 Score: 0.609715702191373 Low Score: -0.7290799842462192 Iteration: 78 Score: 0.6153469903741415 Low Score: -0.7290799842462192 Iteration: 79 Score: 0.5922649360716807 Low Score: -0.7290799842462192 Iteration: 80 Score: 0.7113765269529946 Low Score: -0.7290799842462192 Iteration: 81 Score: -0.3871957459786124 Low Score: -0.7290799842462192 Iteration: 82 Score: -0.38361388833984567 Low Score: -0.7290799842462192 Iteration: 83 Score: -0.1841383911283785 Low Score: -0.7290799842462192 Iteration: 84 Score: -0.3111876842548229 Low Score: -0.7290799842462192 Iteration: 85 Score: -0.42308180652166527 Low Score: -0.7290799842462192 Iteration: 86 Score: -0.42235010607063295 Low Score: -0.7290799842462192 Iteration: 87 Score: -0.5260189964505786 Low Score: -0.7290799842462192 Iteration: 88 Score: -0.5566703987521242 Low Score: -0.7290799842462192 Iteration: 89 Score: -0.7020956322840091 Low Score: -0.7290799842462192 Iteration: 90 Score: -0.6514970124528761 Low Score: -0.7290799842462192 Iteration: 91 Score: -0.6373018756750444 Low Score: -0.7290799842462192 Iteration: 92 Score: -0.6622069285078656 Low Score: -0.7290799842462192 Iteration: 93 Score: -0.21622912961723983 Low Score: -0.7290799842462192 Iteration: 94 Score: -0.26286962938899006 Low Score: -0.7290799842462192 Iteration: 95 Score: -0.3259459032513661 Low Score: -0.7290799842462192 Iteration: 96 Score: -0.3307427156282481 Low Score: -0.7290799842462192 Iteration: 97 Score: -0.3270698258138056 Low Score: -0.7290799842462192 Iteration: 98 Score: 4.022173766118587 Low Score: -0.7290799842462192 Iteration: 99 Score: -0.32719999956697343 Low Score: -0.7290799842462192 3775.511701096452 Residue 5: LYS (LYS, K): Base: LYS Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE METALBINDING SIDECHAIN_AMINE ALPHA_AA L_AA Variant types: Main-chain atoms: N CA C Backbone atoms: N CA C O H HA Side-chain atoms: CB CG CD CE NZ 1HB 2HB 1HG 2HG 1HD 2HD 1HE 2HE 1HZ 2HZ 3HZ Atom Coordinates: N : 20.315, 43.835, 78.015 CA : 20.418, 42.863, 79.118 C : 19.697, 43.46, 80.329 O : 20.096, 44.486, 80.897 CB : 21.858, 42.487, 79.491 CG : 22.791, 42.176, 78.316 CD : 22.406, 40.943, 77.485 CE : 23.009, 40.932, 76.075 NZ : 22.748, 42.169, 75.307 H : 21.0493, 44.5172, 77.8902 HA : 19.9193, 41.9417, 78.815 1HB : 22.3125, 43.3019, 80.0551 2HB : 21.8492, 41.6078, 80.1356 1HG : 22.8124, 43.0262, 77.6332 2HG : 23.8008, 42.0064, 78.6884 1HD : 22.7418, 40.0399, 77.9965 2HD : 21.3219, 40.8985, 77.3807 1HE : 24.088, 40.801, 76.1421 2HE : 22.5982, 40.0953, 75.5101 1HZ : 23.1708, 42.0938, 74.3926 2HZ : 21.751, 42.2999, 75.2069 3HZ : 23.1434, 42.9592, 75.7961 Mirrored relative to coordinates in ResidueType: FALSE Residue 5: LYS (LYS, K): Base: LYS Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE SIDECHAIN_AMINE ALPHA_AA L_AA Variant types: Main-chain atoms: N CA C Backbone atoms: N CA C O H Side-chain atoms: CB CEN Atom Coordinates: N : 20.315, 43.835, 78.015 CA : 20.418, 42.863, 79.118 C : 19.697, 43.46, 80.329 O : 20.096, 44.486, 80.897 CB : 21.8754, 42.543, 79.454 CEN: 23.4957, 41.1851, 79.3707 H : 21.0493, 44.5172, 77.8902 Mirrored relative to coordinates in ResidueType: FALSE -104.17784121598451 Residue 5: LYS (LYS, K): Base: LYS Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE METALBINDING SIDECHAIN_AMINE ALPHA_AA L_AA Variant types: Main-chain atoms: N CA C Backbone atoms: N CA C O H HA Side-chain atoms: CB CG CD CE NZ 1HB 2HB 1HG 2HG 1HD 2HD 1HE 2HE 1HZ 2HZ 3HZ Atom Coordinates: N : 20.315, 43.835, 78.015 CA : 20.418, 42.863, 79.118 C : 19.697, 43.46, 80.329 O : 20.096, 44.486, 80.897 CB : 21.8754, 42.5429, 79.4539 CG : 22.8944, 43.244, 78.5655 CD : 22.2113, 44.1202, 77.5262 CE : 20.6967, 44.0574, 77.6573 NZ : 20.2706, 43.1587, 78.7642 H : 21.0493, 44.5172, 77.8902 HA : 19.9306, 41.9373, 78.8101 1HB : 22.0814, 42.8255, 80.4867 2HB : 22.0409, 41.4686, 79.3693 1HG : 23.5468, 43.8654, 79.1801 2HG : 23.5056, 42.4999, 78.0558 1HD : 22.5361, 45.154, 77.6512 2HD : 22.4937, 43.7874, 76.5274 1HE : 20.3065, 45.0564, 77.8461 2HE : 20.2655, 43.6934, 76.7248 1HZ : 19.2619, 43.1443, 78.8176 2HZ : 20.6116, 42.2236, 78.5898 3HZ : 20.6485, 43.497, 79.6375 Mirrored relative to coordinates in ResidueType: FALSE core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.05515 seconds. core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.import_pose.import_pose: File '../test/data/workshops/6Q21.clean.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.177533 seconds to load from binary core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.018955 seconds. basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/workshops/aat000_03_05.200_v1_3 Finished Workshop4test in 0:00:09.145132

mac.clang.python310.PyRosetta.unit.Workshop5test 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Mover name: PyMOLMover, Mover type: MoverBase, Mover current tag:NoTag Keep history: True Update energy: False Last packet sent time: 1.72574e+09 Update interval: 0 Link: max packet size: 7678 sent count: 2 socket handle: 3 uuid shorts: 0 0 0 0 0 0 0 0 socket address family:  socket address address: 16777343 : 127.0.0.1 socket address port: 59645 : 65000 socket max_packet_size: 7678 Mover name: Small, Mover type: Small, Mover current tag:NoTag Max angle for helices (H): 5 Max angle for strands (E): 5 Max angle for loops (L): 5 Temperature factor (kT): 1 Number of moves: 1 Mover name: Shear, Mover type: Shear, Mover current tag:NoTag Max angle for helices (H): 0 Max angle for strands (E): 5 Max angle for loops (L): 6 Temperature factor (kT): 1 Number of moves: 1 ------------------------------- resnum Type TRUE/FALSE ------------------------------- DEFAULT BB FALSE DEFAULT SC FALSE DEFAULT NU FALSE DEFAULT BRANCH FALSE 050 BB TRUE 051 BB TRUE ------------------------------- jumpnum Type TRUE/FALSE ------------------------------- DEFAULT JUMP FALSE ------------------------------- resnum atomnum Type TRUE/FALSE ------------------------------- DEFAULT PHI FALSE DEFAULT THETA FALSE DEFAULT D FALSE DEFAULT RB1 FALSE DEFAULT RB2 FALSE DEFAULT RB3 FALSE DEFAULT RB4 FALSE DEFAULT RB5 FALSE DEFAULT RB6 FALSE ------------------------------- Mover name: MinMover, Mover type: MinMover, Mover current tag:NoTag Minimization type: lbfgs_armijo_nonmonotone Scorefunction: ref2015 Score tolerance: 0.01 Nb list: True Deriv check: False Movemap: ------------------------------- resnum Type TRUE/FALSE ------------------------------- DEFAULT BB FALSE DEFAULT SC FALSE DEFAULT NU FALSE DEFAULT BRANCH FALSE 040 BB TRUE 041 BB TRUE 042 BB TRUE 043 BB TRUE 044 BB TRUE 045 BB TRUE 046 BB TRUE 047 BB TRUE 048 BB TRUE 049 BB TRUE 050 BB TRUE 051 BB TRUE 052 BB TRUE 053 BB TRUE 054 BB TRUE 055 BB TRUE 056 BB TRUE 057 BB TRUE 058 BB TRUE 059 BB TRUE 060 BB TRUE ------------------------------- jumpnum Type TRUE/FALSE ------------------------------- DEFAULT JUMP FALSE ------------------------------- resnum atomnum Type TRUE/FALSE ------------------------------- DEFAULT PHI FALSE DEFAULT THETA FALSE DEFAULT D FALSE DEFAULT RB1 FALSE DEFAULT RB2 FALSE DEFAULT RB3 FALSE DEFAULT RB4 FALSE DEFAULT RB5 FALSE DEFAULT RB6 FALSE ------------------------------- 1 0.5 Mover name: SequenceMover, Mover type: MoverBase, Mover current tag: NoTag 3 movers are contained in the following order: Mover[1]: Small Mover[2]: Shear Mover[3]: MinMover Mover name: TrialMover, Mover type: MoverBase, Mover current tag: NoTag Mover being tried: 0x600007cfd5e0 Moves were accepted: 0 times. Acceptance rate: 0 MonteCarlo: 0x600007da7740 Mover name: RepeatMover, Mover type: RepeatMover, Mover current tag: NoTag Mover being repeated: TrialMover, nmoves: 2 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.943937 seconds. core.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: Found disulfide between residues 235 308 core.conformation.Conformation: Found disulfide between residues 359 415 core.conformation.Conformation: Found disulfide between residues 457 522 core.conformation.Conformation: Found disulfide between residues 568 628 core.conformation.Conformation: Found disulfide between residues 669 742 core.conformation.Conformation: Found disulfide between residues 793 849 core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.203322 seconds to load from binary core.pack.pack_rotamers: built 85 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 142.844 142.844 protocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.moves.MonteCarlo: MC: 1 142.844 142.844 142.844 142.844 0 0 0 accepted score beat low protocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.TrialMover: Acceptance rate: 0.5 protocols.moves.MonteCarlo: MC: 1 -245.18 -245.18 -245.18 -245.18 0 0 0 accepted score beat low protocols.moves.TrialCounter: Small trials= 2; accepts= 0.5000; energy_drop/trial= -194.01213 protocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.moves.MonteCarlo: MC: 1 -303.474 -303.474 -303.474 -303.474 0 0 0 accepted score beat low protocols.moves.TrialCounter: Small trials= 2; accepts= 0.5000; energy_drop/trial= -194.01213 protocols.moves.TrialCounter: SmallShearMinMov trials= 2; accepts= 1.0000; energy_drop/trial= -29.14699 protocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000 protocols.relax.ClassicRelax: Setting up default relax setting Finished Workshop5test in 0:00:12.365221

mac.clang.python310.PyRosetta.unit.Workshop6test 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 FALSE FALSE ASP:NtermProteinFull 2 FALSE FALSE ILE 3 FALSE FALSE LEU 4 FALSE FALSE LEU 5 FALSE FALSE THR 6 FALSE FALSE GLN 7 FALSE FALSE SER 8 FALSE FALSE PRO 9 FALSE FALSE VAL 10 FALSE FALSE ILE 11 FALSE FALSE LEU 12 FALSE FALSE SER 13 FALSE FALSE VAL 14 FALSE FALSE SER 15 FALSE FALSE PRO 16 FALSE FALSE GLY 17 FALSE FALSE GLU 18 FALSE FALSE ARG 19 FALSE FALSE VAL 20 FALSE FALSE SER 21 FALSE FALSE PHE 22 FALSE FALSE SER 23 FALSE FALSE 24 FALSE FALSE ARG 25 FALSE FALSE ALA 26 FALSE FALSE SER 27 FALSE FALSE GLN 28 FALSE FALSE SER 29 FALSE FALSE ILE 30 FALSE FALSE GLY 31 FALSE FALSE THR 32 FALSE FALSE ASN 33 FALSE FALSE ILE 34 FALSE FALSE HIS,HIS_D 35 FALSE FALSE TRP 36 FALSE FALSE TYR 37 FALSE FALSE GLN 38 FALSE FALSE GLN 39 FALSE FALSE ARG 40 FALSE FALSE THR 41 FALSE FALSE ASN 42 FALSE FALSE GLY 43 FALSE FALSE SER 44 FALSE FALSE PRO 45 FALSE FALSE ARG 46 FALSE FALSE LEU 47 FALSE FALSE LEU 48 FALSE FALSE ILE 49 TRUE FALSE LYS 50 FALSE FALSE TYR 51 FALSE FALSE ALA 52 FALSE FALSE SER 53 FALSE FALSE GLU 54 FALSE FALSE SER 55 FALSE FALSE ILE 56 FALSE FALSE SER 57 FALSE FALSE GLY 58 FALSE FALSE ILE 59 FALSE FALSE PRO 60 FALSE FALSE SER 61 FALSE FALSE ARG 62 FALSE FALSE PHE 63 FALSE FALSE SER 64 FALSE FALSE GLY 65 FALSE FALSE SER 66 FALSE FALSE GLY 67 FALSE FALSE SER 68 FALSE FALSE GLY 69 FALSE FALSE THR 70 FALSE FALSE ASP 71 FALSE FALSE PHE 72 FALSE FALSE THR 73 FALSE FALSE LEU 74 FALSE FALSE SER 75 FALSE FALSE ILE 76 FALSE FALSE ASN 77 FALSE FALSE SER 78 FALSE FALSE VAL 79 FALSE FALSE GLU 80 FALSE FALSE SER 81 FALSE FALSE GLU 82 FALSE FALSE ASP 83 FALSE FALSE ILE 84 FALSE FALSE ALA 85 FALSE FALSE ASP 86 FALSE FALSE TYR 87 FALSE FALSE TYR 88 FALSE FALSE 89 FALSE FALSE GLN 90 FALSE FALSE GLN 91 FALSE FALSE ASN 92 FALSE FALSE ASN 93 FALSE FALSE ASN 94 FALSE FALSE TRP 95 FALSE FALSE PRO 96 FALSE FALSE THR 97 FALSE FALSE THR 98 FALSE FALSE PHE 99 FALSE FALSE GLY 100 FALSE FALSE ALA 101 FALSE FALSE GLY 102 FALSE FALSE THR 103 FALSE FALSE LYS 104 FALSE FALSE LEU 105 FALSE FALSE GLU 106 FALSE FALSE LEU 107 FALSE FALSE LYS 108 FALSE FALSE ARG 109 FALSE FALSE THR 110 FALSE FALSE VAL 111 FALSE FALSE ALA 112 FALSE FALSE ALA 113 FALSE FALSE PRO 114 FALSE FALSE SER 115 FALSE FALSE VAL 116 FALSE FALSE PHE 117 FALSE FALSE ILE 118 FALSE FALSE PHE 119 FALSE FALSE PRO 120 FALSE FALSE PRO 121 FALSE FALSE SER 122 FALSE FALSE ASP 123 FALSE FALSE GLU 124 FALSE FALSE GLN 125 FALSE FALSE LEU 126 FALSE FALSE LYS 127 FALSE FALSE SER 128 FALSE FALSE GLY 129 FALSE FALSE THR 130 FALSE FALSE ALA 131 FALSE FALSE SER 132 FALSE FALSE VAL 133 FALSE FALSE VAL 134 FALSE FALSE 135 FALSE FALSE LEU 136 FALSE FALSE LEU 137 FALSE FALSE ASN 138 FALSE FALSE ASN 139 FALSE FALSE PHE 140 FALSE FALSE TYR 141 FALSE FALSE PRO 142 FALSE FALSE ARG 143 FALSE FALSE GLU 144 FALSE FALSE ALA 145 FALSE FALSE LYS 146 FALSE FALSE VAL 147 FALSE FALSE GLN 148 FALSE FALSE TRP 149 FALSE FALSE LYS 150 FALSE FALSE VAL 151 FALSE FALSE ASP 152 FALSE FALSE ASN 153 FALSE FALSE ALA 154 FALSE FALSE LEU 155 FALSE FALSE GLN 156 FALSE FALSE SER 157 FALSE FALSE GLY 158 FALSE FALSE ASN 159 FALSE FALSE SER 160 FALSE FALSE GLN 161 FALSE FALSE GLU 162 FALSE FALSE SER 163 FALSE FALSE VAL 164 FALSE FALSE THR 165 FALSE FALSE GLU 166 FALSE FALSE GLN 167 FALSE FALSE ASP 168 FALSE FALSE SER 169 FALSE FALSE LYS 170 FALSE FALSE ASP 171 FALSE FALSE SER 172 FALSE FALSE THR 173 FALSE FALSE TYR 174 FALSE FALSE SER 175 FALSE FALSE LEU 176 FALSE FALSE SER 177 FALSE FALSE SER 178 FALSE FALSE THR 179 FALSE FALSE LEU 180 FALSE FALSE THR 181 FALSE FALSE LEU 182 FALSE FALSE SER 183 FALSE FALSE LYS 184 FALSE FALSE ALA 185 FALSE FALSE ASP 186 FALSE FALSE TYR 187 FALSE FALSE GLU 188 FALSE FALSE LYS 189 FALSE FALSE HIS,HIS_D 190 FALSE FALSE LYS 191 FALSE FALSE VAL 192 FALSE FALSE TYR 193 FALSE FALSE ALA 194 FALSE FALSE 195 FALSE FALSE GLU 196 FALSE FALSE VAL 197 FALSE FALSE THR 198 FALSE FALSE HIS,HIS_D 199 FALSE FALSE GLN 200 FALSE FALSE GLY 201 FALSE FALSE LEU 202 FALSE FALSE SER 203 FALSE FALSE SER 204 FALSE FALSE PRO 205 FALSE FALSE VAL 206 FALSE FALSE THR 207 FALSE FALSE LYS 208 FALSE FALSE SER 209 FALSE FALSE PHE 210 FALSE FALSE ASN 211 FALSE FALSE ARG 212 FALSE FALSE GLY 213 FALSE FALSE ALA:CtermProteinFull 214 FALSE FALSE GLN:NtermProteinFull 215 FALSE FALSE VAL 216 FALSE FALSE GLN 217 FALSE FALSE LEU 218 FALSE FALSE LYS 219 FALSE FALSE GLN 220 FALSE FALSE SER 221 FALSE FALSE GLY 222 FALSE FALSE PRO 223 FALSE FALSE GLY 224 FALSE FALSE LEU 225 FALSE FALSE VAL 226 FALSE FALSE GLN 227 FALSE FALSE PRO 228 FALSE FALSE SER 229 FALSE FALSE GLN 230 FALSE FALSE SER 231 FALSE FALSE LEU 232 FALSE FALSE SER 233 FALSE FALSE ILE 234 FALSE FALSE THR 235 FALSE FALSE 236 FALSE FALSE THR 237 FALSE FALSE VAL 238 FALSE FALSE SER 239 FALSE FALSE GLY 240 FALSE FALSE PHE 241 FALSE FALSE SER 242 FALSE FALSE LEU 243 FALSE FALSE THR 244 FALSE FALSE ASN 245 FALSE FALSE TYR 246 FALSE FALSE GLY 247 FALSE FALSE VAL 248 FALSE FALSE HIS,HIS_D 249 FALSE FALSE TRP 250 FALSE FALSE VAL 251 FALSE FALSE ARG 252 FALSE FALSE GLN 253 FALSE FALSE SER 254 FALSE FALSE PRO 255 FALSE FALSE GLY 256 FALSE FALSE LYS 257 FALSE FALSE GLY 258 FALSE FALSE LEU 259 FALSE FALSE GLU 260 FALSE FALSE TRP 261 FALSE FALSE LEU 262 FALSE FALSE GLY 263 FALSE FALSE VAL 264 FALSE FALSE ILE 265 FALSE FALSE TRP 266 FALSE FALSE SER 267 FALSE FALSE GLY 268 FALSE FALSE GLY 269 FALSE FALSE ASN 270 FALSE FALSE THR 271 FALSE FALSE ASP 272 FALSE FALSE TYR 273 FALSE FALSE ASN 274 FALSE FALSE THR 275 FALSE FALSE PRO 276 FALSE FALSE PHE 277 FALSE FALSE THR 278 FALSE FALSE SER 279 FALSE FALSE ARG 280 FALSE FALSE LEU 281 FALSE FALSE SER 282 FALSE FALSE ILE 283 FALSE FALSE ASN 284 FALSE FALSE LYS 285 FALSE FALSE ASP 286 FALSE FALSE ASN 287 FALSE FALSE SER 288 FALSE FALSE LYS 289 FALSE FALSE SER 290 FALSE FALSE GLN 291 FALSE FALSE VAL 292 FALSE FALSE PHE 293 FALSE FALSE PHE 294 FALSE FALSE LYS 295 FALSE FALSE MET 296 FALSE FALSE ASN 297 FALSE FALSE SER 298 FALSE FALSE LEU 299 FALSE FALSE GLN 300 FALSE FALSE SER 301 FALSE FALSE ASN 302 FALSE FALSE ASP 303 FALSE FALSE THR 304 FALSE FALSE ALA 305 FALSE FALSE ILE 306 FALSE FALSE TYR 307 FALSE FALSE TYR 308 FALSE FALSE 309 FALSE FALSE ALA 310 FALSE FALSE ARG 311 FALSE FALSE ALA 312 FALSE FALSE LEU 313 FALSE FALSE THR 314 FALSE FALSE TYR 315 FALSE FALSE TYR 316 FALSE FALSE ASP 317 FALSE FALSE TYR 318 FALSE FALSE GLU 319 FALSE FALSE PHE 320 FALSE FALSE ALA 321 FALSE FALSE TYR 322 FALSE FALSE TRP 323 FALSE FALSE GLY 324 FALSE FALSE GLN 325 FALSE FALSE GLY 326 FALSE FALSE THR 327 FALSE FALSE LEU 328 FALSE FALSE VAL 329 FALSE FALSE THR 330 FALSE FALSE VAL 331 FALSE FALSE SER 332 FALSE FALSE ALA 333 FALSE FALSE ALA 334 FALSE FALSE SER 335 FALSE FALSE THR 336 FALSE FALSE LYS 337 FALSE FALSE GLY 338 FALSE FALSE PRO 339 FALSE FALSE SER 340 FALSE FALSE VAL 341 FALSE FALSE PHE 342 FALSE FALSE PRO 343 FALSE FALSE LEU 344 FALSE FALSE ALA 345 FALSE FALSE PRO 346 FALSE FALSE SER 347 FALSE FALSE SER 348 FALSE FALSE LYS 349 FALSE FALSE SER 350 FALSE FALSE THR 351 FALSE FALSE SER 352 FALSE FALSE GLY 353 FALSE FALSE GLY 354 FALSE FALSE THR 355 FALSE FALSE ALA 356 FALSE FALSE ALA 357 FALSE FALSE LEU 358 FALSE FALSE GLY 359 FALSE FALSE 360 FALSE FALSE LEU 361 FALSE FALSE VAL 362 FALSE FALSE LYS 363 FALSE FALSE ASP 364 FALSE FALSE TYR 365 FALSE FALSE PHE 366 FALSE FALSE PRO 367 FALSE FALSE GLU 368 FALSE FALSE PRO 369 FALSE FALSE VAL 370 FALSE FALSE THR 371 FALSE FALSE VAL 372 FALSE FALSE SER 373 FALSE FALSE TRP 374 FALSE FALSE ASN 375 FALSE FALSE SER 376 FALSE FALSE GLY 377 FALSE FALSE ALA 378 FALSE FALSE LEU 379 FALSE FALSE THR 380 FALSE FALSE SER 381 FALSE FALSE GLY 382 FALSE FALSE VAL 383 FALSE FALSE HIS,HIS_D 384 FALSE FALSE THR 385 FALSE FALSE PHE 386 FALSE FALSE PRO 387 FALSE FALSE ALA 388 FALSE FALSE VAL 389 FALSE FALSE LEU 390 FALSE FALSE GLN 391 FALSE FALSE SER 392 FALSE FALSE SER 393 FALSE FALSE GLY 394 FALSE FALSE LEU 395 FALSE FALSE TYR 396 FALSE FALSE SER 397 FALSE FALSE LEU 398 FALSE FALSE SER 399 FALSE FALSE SER 400 FALSE FALSE VAL 401 FALSE FALSE VAL 402 FALSE FALSE THR 403 FALSE FALSE VAL 404 FALSE FALSE PRO 405 FALSE FALSE SER 406 FALSE FALSE SER 407 FALSE FALSE SER 408 FALSE FALSE LEU 409 FALSE FALSE GLY 410 FALSE FALSE THR 411 FALSE FALSE GLN 412 FALSE FALSE THR 413 FALSE FALSE TYR 414 FALSE FALSE ILE 415 FALSE FALSE 416 FALSE FALSE ASN 417 FALSE FALSE VAL 418 FALSE FALSE ASN 419 FALSE FALSE HIS,HIS_D 420 FALSE FALSE LYS 421 FALSE FALSE PRO 422 FALSE FALSE SER 423 FALSE FALSE ASN 424 FALSE FALSE THR 425 FALSE FALSE LYS 426 FALSE FALSE VAL 427 FALSE FALSE ASP 428 FALSE FALSE LYS 429 FALSE FALSE ARG 430 FALSE FALSE VAL 431 FALSE FALSE GLU 432 FALSE FALSE PRO 433 FALSE FALSE LYS 434 FALSE FALSE SER:CtermProteinFull 435 FALSE FALSE ASP:NtermProteinFull 436 FALSE FALSE ILE 437 FALSE FALSE LEU 438 FALSE FALSE LEU 439 FALSE FALSE THR 440 FALSE FALSE GLN 441 FALSE FALSE SER 442 FALSE FALSE PRO 443 FALSE FALSE VAL 444 FALSE FALSE ILE 445 FALSE FALSE LEU 446 FALSE FALSE SER 447 FALSE FALSE VAL 448 FALSE FALSE SER 449 FALSE FALSE PRO 450 FALSE FALSE GLY 451 FALSE FALSE GLU 452 FALSE FALSE ARG 453 FALSE FALSE VAL 454 FALSE FALSE SER 455 FALSE FALSE PHE 456 FALSE FALSE SER 457 FALSE FALSE 458 FALSE FALSE ARG 459 FALSE FALSE ALA 460 FALSE FALSE SER 461 FALSE FALSE GLN 462 FALSE FALSE SER 463 FALSE FALSE ILE 464 FALSE FALSE GLY 465 FALSE FALSE THR 466 FALSE FALSE ASN 467 FALSE FALSE ILE 468 FALSE FALSE HIS,HIS_D 469 FALSE FALSE TRP 470 FALSE FALSE TYR 471 FALSE FALSE GLN 472 FALSE FALSE GLN 473 FALSE FALSE ARG 474 FALSE FALSE THR 475 FALSE FALSE ASN 476 FALSE FALSE GLY 477 FALSE FALSE SER 478 FALSE FALSE PRO 479 FALSE FALSE ARG 480 FALSE FALSE LEU 481 FALSE FALSE LEU 482 FALSE FALSE ILE 483 FALSE FALSE LYS 484 FALSE FALSE TYR 485 FALSE FALSE ALA 486 FALSE FALSE SER 487 FALSE FALSE GLU 488 FALSE FALSE SER 489 FALSE FALSE ILE 490 FALSE FALSE SER 491 FALSE FALSE GLY 492 FALSE FALSE ILE 493 FALSE FALSE PRO 494 FALSE FALSE SER 495 FALSE FALSE ARG 496 FALSE FALSE PHE 497 FALSE FALSE SER 498 FALSE FALSE GLY 499 FALSE FALSE SER 500 FALSE FALSE GLY 501 FALSE FALSE SER 502 FALSE FALSE GLY 503 FALSE FALSE THR 504 FALSE FALSE ASP 505 FALSE FALSE PHE 506 FALSE FALSE THR 507 FALSE FALSE LEU 508 FALSE FALSE SER 509 FALSE FALSE ILE 510 FALSE FALSE ASN 511 FALSE FALSE SER 512 FALSE FALSE VAL 513 FALSE FALSE GLU 514 FALSE FALSE SER 515 FALSE FALSE GLU 516 FALSE FALSE ASP 517 FALSE FALSE ILE 518 FALSE FALSE ALA 519 FALSE FALSE ASP 520 FALSE FALSE TYR 521 FALSE FALSE TYR 522 FALSE FALSE 523 FALSE FALSE GLN 524 FALSE FALSE GLN 525 FALSE FALSE ASN 526 FALSE FALSE ASN 527 FALSE FALSE ASN 528 FALSE FALSE TRP 529 FALSE FALSE PRO 530 FALSE FALSE THR 531 FALSE FALSE THR 532 FALSE FALSE PHE 533 FALSE FALSE GLY 534 FALSE FALSE ALA 535 FALSE FALSE GLY 536 FALSE FALSE THR 537 FALSE FALSE LYS 538 FALSE FALSE LEU 539 FALSE FALSE GLU 540 FALSE FALSE LEU 541 FALSE FALSE LYS 542 FALSE FALSE ARG 543 FALSE FALSE THR 544 FALSE FALSE VAL 545 FALSE FALSE ALA 546 FALSE FALSE ALA 547 FALSE FALSE PRO 548 FALSE FALSE SER 549 FALSE FALSE VAL 550 FALSE FALSE PHE 551 FALSE FALSE ILE 552 FALSE FALSE PHE 553 FALSE FALSE PRO 554 FALSE FALSE PRO 555 FALSE FALSE SER 556 FALSE FALSE ASP 557 FALSE FALSE GLU 558 FALSE FALSE GLN 559 FALSE FALSE LEU 560 FALSE FALSE LYS 561 FALSE FALSE SER 562 FALSE FALSE GLY 563 FALSE FALSE THR 564 FALSE FALSE ALA 565 FALSE FALSE SER 566 FALSE FALSE VAL 567 FALSE FALSE VAL 568 FALSE FALSE 569 FALSE FALSE LEU 570 FALSE FALSE LEU 571 FALSE FALSE ASN 572 FALSE FALSE ASN 573 FALSE FALSE PHE 574 FALSE FALSE TYR 575 FALSE FALSE PRO 576 FALSE FALSE ARG 577 FALSE FALSE GLU 578 FALSE FALSE ALA 579 FALSE FALSE LYS 580 FALSE FALSE VAL 581 FALSE FALSE GLN 582 FALSE FALSE TRP 583 FALSE FALSE LYS 584 FALSE FALSE VAL 585 FALSE FALSE ASP 586 FALSE FALSE ASN 587 FALSE FALSE ALA 588 FALSE FALSE LEU 589 FALSE FALSE GLN 590 FALSE FALSE SER 591 FALSE FALSE GLY 592 FALSE FALSE ASN 593 FALSE FALSE SER 594 FALSE FALSE GLN 595 FALSE FALSE GLU 596 FALSE FALSE SER 597 FALSE FALSE VAL 598 FALSE FALSE THR 599 FALSE FALSE GLU 600 FALSE FALSE GLN 601 FALSE FALSE ASP 602 FALSE FALSE SER 603 FALSE FALSE LYS 604 FALSE FALSE ASP 605 FALSE FALSE SER 606 FALSE FALSE THR 607 FALSE FALSE TYR 608 FALSE FALSE SER 609 FALSE FALSE LEU 610 FALSE FALSE SER 611 FALSE FALSE SER 612 FALSE FALSE THR 613 FALSE FALSE LEU 614 FALSE FALSE THR 615 FALSE FALSE LEU 616 FALSE FALSE SER 617 FALSE FALSE LYS 618 FALSE FALSE ALA 619 FALSE FALSE ASP 620 FALSE FALSE TYR 621 FALSE FALSE GLU 622 FALSE FALSE LYS 623 FALSE FALSE HIS,HIS_D 624 FALSE FALSE LYS 625 FALSE FALSE VAL 626 FALSE FALSE TYR 627 FALSE FALSE ALA 628 FALSE FALSE 629 FALSE FALSE GLU 630 FALSE FALSE VAL 631 FALSE FALSE THR 632 FALSE FALSE HIS,HIS_D 633 FALSE FALSE GLN 634 FALSE FALSE GLY 635 FALSE FALSE LEU 636 FALSE FALSE SER 637 FALSE FALSE SER 638 FALSE FALSE PRO 639 FALSE FALSE VAL 640 FALSE FALSE THR 641 FALSE FALSE LYS 642 FALSE FALSE SER 643 FALSE FALSE PHE 644 FALSE FALSE ASN 645 FALSE FALSE ARG 646 FALSE FALSE GLY 647 FALSE FALSE ALA:CtermProteinFull 648 FALSE FALSE GLN:NtermProteinFull 649 FALSE FALSE VAL 650 FALSE FALSE GLN 651 FALSE FALSE LEU 652 FALSE FALSE LYS 653 FALSE FALSE GLN 654 FALSE FALSE SER 655 FALSE FALSE GLY 656 FALSE FALSE PRO 657 FALSE FALSE GLY 658 FALSE FALSE LEU 659 FALSE FALSE VAL 660 FALSE FALSE GLN 661 FALSE FALSE PRO 662 FALSE FALSE SER 663 FALSE FALSE GLN 664 FALSE FALSE SER 665 FALSE FALSE LEU 666 FALSE FALSE SER 667 FALSE FALSE ILE 668 FALSE FALSE THR 669 FALSE FALSE 670 FALSE FALSE THR 671 FALSE FALSE VAL 672 FALSE FALSE SER 673 FALSE FALSE GLY 674 FALSE FALSE PHE 675 FALSE FALSE SER 676 FALSE FALSE LEU 677 FALSE FALSE THR 678 FALSE FALSE ASN 679 FALSE FALSE TYR 680 FALSE FALSE GLY 681 FALSE FALSE VAL 682 FALSE FALSE HIS,HIS_D 683 FALSE FALSE TRP 684 FALSE FALSE VAL 685 FALSE FALSE ARG 686 FALSE FALSE GLN 687 FALSE FALSE SER 688 FALSE FALSE PRO 689 FALSE FALSE GLY 690 FALSE FALSE LYS 691 FALSE FALSE GLY 692 FALSE FALSE LEU 693 FALSE FALSE GLU 694 FALSE FALSE TRP 695 FALSE FALSE LEU 696 FALSE FALSE GLY 697 FALSE FALSE VAL 698 FALSE FALSE ILE 699 FALSE FALSE TRP 700 FALSE FALSE SER 701 FALSE FALSE GLY 702 FALSE FALSE GLY 703 FALSE FALSE ASN 704 FALSE FALSE THR 705 FALSE FALSE ASP 706 FALSE FALSE TYR 707 FALSE FALSE ASN 708 FALSE FALSE THR 709 FALSE FALSE PRO 710 FALSE FALSE PHE 711 FALSE FALSE THR 712 FALSE FALSE SER 713 FALSE FALSE ARG 714 FALSE FALSE LEU 715 FALSE FALSE SER 716 FALSE FALSE ILE 717 FALSE FALSE ASN 718 FALSE FALSE LYS 719 FALSE FALSE ASP 720 FALSE FALSE ASN 721 FALSE FALSE SER 722 FALSE FALSE LYS 723 FALSE FALSE SER 724 FALSE FALSE GLN 725 FALSE FALSE VAL 726 FALSE FALSE PHE 727 FALSE FALSE PHE 728 FALSE FALSE LYS 729 FALSE FALSE MET 730 FALSE FALSE ASN 731 FALSE FALSE SER 732 FALSE FALSE LEU 733 FALSE FALSE GLN 734 FALSE FALSE SER 735 FALSE FALSE ASN 736 FALSE FALSE ASP 737 FALSE FALSE THR 738 FALSE FALSE ALA 739 FALSE FALSE ILE 740 FALSE FALSE TYR 741 FALSE FALSE TYR 742 FALSE FALSE 743 FALSE FALSE ALA 744 FALSE FALSE ARG 745 FALSE FALSE ALA 746 FALSE FALSE LEU 747 FALSE FALSE THR 748 FALSE FALSE TYR 749 FALSE FALSE TYR 750 FALSE FALSE ASP 751 FALSE FALSE TYR 752 FALSE FALSE GLU 753 FALSE FALSE PHE 754 FALSE FALSE ALA 755 FALSE FALSE TYR 756 FALSE FALSE TRP 757 FALSE FALSE GLY 758 FALSE FALSE GLN 759 FALSE FALSE GLY 760 FALSE FALSE THR 761 FALSE FALSE LEU 762 FALSE FALSE VAL 763 FALSE FALSE THR 764 FALSE FALSE VAL 765 FALSE FALSE SER 766 FALSE FALSE ALA 767 FALSE FALSE ALA 768 FALSE FALSE SER 769 FALSE FALSE THR 770 FALSE FALSE LYS 771 FALSE FALSE GLY 772 FALSE FALSE PRO 773 FALSE FALSE SER 774 FALSE FALSE VAL 775 FALSE FALSE PHE 776 FALSE FALSE PRO 777 FALSE FALSE LEU 778 FALSE FALSE ALA 779 FALSE FALSE PRO 780 FALSE FALSE SER 781 FALSE FALSE SER 782 FALSE FALSE LYS 783 FALSE FALSE SER 784 FALSE FALSE THR 785 FALSE FALSE SER 786 FALSE FALSE GLY 787 FALSE FALSE GLY 788 FALSE FALSE THR 789 FALSE FALSE ALA 790 FALSE FALSE ALA 791 FALSE FALSE LEU 792 FALSE FALSE GLY 793 FALSE FALSE 794 FALSE FALSE LEU 795 FALSE FALSE VAL 796 FALSE FALSE LYS 797 FALSE FALSE ASP 798 FALSE FALSE TYR 799 FALSE FALSE PHE 800 FALSE FALSE PRO 801 FALSE FALSE GLU 802 FALSE FALSE PRO 803 FALSE FALSE VAL 804 FALSE FALSE THR 805 FALSE FALSE VAL 806 FALSE FALSE SER 807 FALSE FALSE TRP 808 FALSE FALSE ASN 809 FALSE FALSE SER 810 FALSE FALSE GLY 811 FALSE FALSE ALA 812 FALSE FALSE LEU 813 FALSE FALSE THR 814 FALSE FALSE SER 815 FALSE FALSE GLY 816 FALSE FALSE VAL 817 FALSE FALSE HIS,HIS_D 818 FALSE FALSE THR 819 FALSE FALSE PHE 820 FALSE FALSE PRO 821 FALSE FALSE ALA 822 FALSE FALSE VAL 823 FALSE FALSE LEU 824 FALSE FALSE GLN 825 FALSE FALSE SER 826 FALSE FALSE SER 827 FALSE FALSE GLY 828 FALSE FALSE LEU 829 FALSE FALSE TYR 830 FALSE FALSE SER 831 FALSE FALSE LEU 832 FALSE FALSE SER 833 FALSE FALSE SER 834 FALSE FALSE VAL 835 FALSE FALSE VAL 836 FALSE FALSE THR 837 FALSE FALSE VAL 838 FALSE FALSE PRO 839 FALSE FALSE SER 840 FALSE FALSE SER 841 FALSE FALSE SER 842 FALSE FALSE LEU 843 FALSE FALSE GLY 844 FALSE FALSE THR 845 FALSE FALSE GLN 846 FALSE FALSE THR 847 FALSE FALSE TYR 848 FALSE FALSE ILE 849 FALSE FALSE 850 FALSE FALSE ASN 851 FALSE FALSE VAL 852 FALSE FALSE ASN 853 FALSE FALSE HIS,HIS_D 854 FALSE FALSE LYS 855 FALSE FALSE PRO 856 FALSE FALSE SER 857 FALSE FALSE ASN 858 FALSE FALSE THR 859 FALSE FALSE LYS 860 FALSE FALSE VAL 861 FALSE FALSE ASP 862 FALSE FALSE LYS 863 FALSE FALSE ARG 864 FALSE FALSE VAL 865 FALSE FALSE GLU 866 FALSE FALSE PRO 867 FALSE FALSE LYS 868 FALSE FALSE SER:CtermProteinFull core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.956503 seconds. core.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: Found disulfide between residues 235 308 core.conformation.Conformation: Found disulfide between residues 359 415 core.conformation.Conformation: Found disulfide between residues 457 522 core.conformation.Conformation: Found disulfide between residues 568 628 core.conformation.Conformation: Found disulfide between residues 669 742 core.conformation.Conformation: Found disulfide between residues 793 849 core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.22122 seconds to load from binary core.pack.pack_rotamers: built 85 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 9 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: Found disulfide between residues 235 308 core.conformation.Conformation: Found disulfide between residues 359 415 core.conformation.Conformation: Found disulfide between residues 457 522 core.conformation.Conformation: Found disulfide between residues 568 628 core.conformation.Conformation: Found disulfide between residues 669 742 core.conformation.Conformation: Found disulfide between residues 793 849 core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.pack_rotamers: built 85 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 16 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph Finished Workshop6test in 0:00:07.977831

mac.clang.python310.PyRosetta.unit.Workshop7test 「click to collapse/expand」

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.03455 seconds. core.import_pose.import_pose: File '../test/data/workshops/complex.start.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 246 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 321 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 321 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 321 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 338 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 338 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 338 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 359 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 359 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 359 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 371 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 371 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 371 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 372 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 372 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 372 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 381 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 381 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 381 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 392 core.conformation.Conformation: Found disulfide between residues 7 137 core.conformation.Conformation: Found disulfide between residues 25 41 core.conformation.Conformation: Found disulfide between residues 109 210 core.conformation.Conformation: Found disulfide between residues 116 183 core.conformation.Conformation: Found disulfide between residues 148 162 core.conformation.Conformation: Found disulfide between residues 173 197 core.conformation.Conformation: Found disulfide between residues 262 309 core.conformation.Conformation: Found disulfide between residues 356 361 core.pack.pack_missing_sidechains: packing residue number 246 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 6 atom name OG1 core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 321 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 334 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 335 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 338 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 348 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 359 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 360 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 371 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 372 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 381 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 383 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.193306 seconds to load from binary core.pack.pack_rotamers: built 209 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt protocols.docking.DockingInitialPerturbation: Sliding Pose components together into contact core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.018695 seconds. protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.46 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Acceptance rate is: 0.3 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.26 core.import_pose.import_pose: File '../test/data/workshops/complex.high.pdb' automatically determined to be of type PDB core.conformation.Conformation: Found disulfide between residues 7 137 core.conformation.Conformation: Found disulfide between residues 25 41 core.conformation.Conformation: Found disulfide between residues 109 210 core.conformation.Conformation: Found disulfide between residues 116 183 core.conformation.Conformation: Found disulfide between residues 148 162 core.conformation.Conformation: Found disulfide between residues 173 197 core.conformation.Conformation: Found disulfide between residues 262 309 core.conformation.Conformation: Found disulfide between residues 356 361 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.1 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.1 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: Translation magnitude: 0.7 protocols.docking.DockingLowRes: Rotation magnitude: 5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.63 protocols.docking.DockingLowRes: Rotation magnitude: 4.5 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.567 protocols.docking.DockingLowRes: Rotation magnitude: 4.05 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.5103 protocols.docking.DockingLowRes: Rotation magnitude: 3.645 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.45927 protocols.docking.DockingLowRes: Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.413343 protocols.docking.DockingLowRes: Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.04 protocols.docking.DockingLowRes: Translation magnitude: 0.372009 protocols.docking.DockingLowRes: Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0 protocols.docking.DockingLowRes: Translation magnitude: 0.334808 protocols.docking.DockingLowRes: Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.06 protocols.docking.DockingLowRes: Translation magnitude: 0.301327 protocols.docking.DockingLowRes: Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.Do┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git FOLD_TREE EDGE 1 223 -1 EDGE 1 224 1 EDGE 224 392 -1 FOLD_TREE EDGE 1 179 -1 EDGE 179 223 -1 EDGE 179 252 1 EDGE 252 224 -1 EDGE 252 392 -1 0.6617414920971024 -0.03498899193021877 -0.7489151941847656 0.003717401098845607 -0.9987450200787071 0.04994562840786065 -0.7497228678426275 -0.03583511283215074 -0.6607809516943858 -33.9748,-19.594,20.9708 _____ Check point 1 _____ Check point 2 _____ Check point 3 Making MinMover... Done Applying MinMover! 7.830221176147461 14.240274487771014 Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_2.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_6.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_4.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_7.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_3.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_8.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_9.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_1.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_0.pdb Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp46ezbq7u_5.pdb done ckingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.08 protocols.docking.DockingLowRes: Translation magnitude: 0.271194 protocols.docking.DockingLowRes: Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Accepted protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Rigid Body Perturbation Rejected protocols.docking.DockingLowRes: Acceptance rate is: 0.02 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 Finished Workshop7test in 0:00:45.136237
WARNING: Sub-test log is too large to be fully displayed here, please visit sub-test「mac.clang.python310.PyRosetta.unit.Workshop7test」page to see full log! core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.03455 seconds. core.import_pose.import_pose: File '../test/data/workshops/complex.start.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 246 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 272 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 286 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 288 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 321 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 321 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 321 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 338 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 338 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 338 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 348 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 359 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 359 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 359 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 360 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 371 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 371 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 371 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 372 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 372 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 372 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 381 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 381 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 381 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 383 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 392 core.conformation.Conformation: Found disulfide between residues 7 137 core.conformation.Conformation: Found disulfide between residues 25 41 core.conformation.Conformation: Found disulfide between residues 109 210 core.conformation.Conformation: Found disulfide between residues 116 183 core.conformation.Conformation: Found disulfide between residues 148 162 core.conformation.Conformation: Found disulfide between residues 173 197 core.conformation.Conformation: Found disulfide between residues 262 309 core.conformation.Conformation: Found disulfide between residues 356 361 core.pack.pack_missing_sidechains: packing residue number 246 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 6 atom name OG1 core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 321 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 334 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 335 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 338 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 348 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 359 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 360 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 371 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 372 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 381 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 383 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.193306 seconds to load from binary core.pack.pack_rotamers: built 209 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt protocols.docking.DockingInitialPerturbation: Sliding Pose components together into contact core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.018695 seconds. protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.Dock

mac.clang.python310.PyRosetta.unit.Workshop8test 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git FOLD_TREE EDGE 1 13 -1 EDGE 13 19 -1 EDGE 13 26 1 EDGE 26 20 -1 EDGE 26 116 -1 Working on decoy: /var/folders/qh/ns_0rqgd36n06gt8yg5zqlkm0002cr/T/tmp2auk_bco_0.pdb core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.91501 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB protocols.loops.loops_main: Added cutpoint variant to residue 19 protocols.loops.loops_main: Added cutpoint variant to residue 20 core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 14 -1 EDGE 14 19 -1 EDGE 14 25 1 EDGE 25 20 -1 EDGE 25 116 -1 core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 14 -1 EDGE 14 19 -1 EDGE 14 25 1 EDGE 25 20 -1 EDGE 25 116 -1 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.024958 seconds. basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 Finished Workshop8test in 0:00:06.096388

mac.clang.python310.PyRosetta.unit.Workshop9_my_shapes 「click to collapse/expand」

/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/Workshop9_my_shapes.py:84: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.core.scoring.methods import ContextIndependentOneBodyEnergy Finished Workshop9_my_shapes in 0:00:02.398917

mac.clang.python310.PyRosetta.unit.Workshop9test 「click to collapse/expand」

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git A subclass of MyShape for a circle. A subclass of MyShape for a square. black black 4 7.0685834705770345 Incrementing phi of residue 1 by15 degrees.... Incrementing phi of residue 10 by45 degrees.... Score of the pose: 0.0 New score of the pose: -20.0 core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.00505 seconds. core.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648 core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: Found disulfide between residues 235 308 core.conformation.Conformation: Found disulfide between residues 359 415 core.conformation.Conformation: Found disulfide between residues 457 522 core.conformation.Conformation: Found disulfide between residues 568 628 core.conformation.Conformation: Found disulfide between residues 669 742 core.conformation.Conformation: Found disulfide between residues 793 849 core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.184228 seconds to load from binary core.pack.pack_rotamers: built 85 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/python/PyRosetta/src/test/Workshop9_my_shapes.py:84: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.core.scoring.methods import ContextIndependentOneBodyEnergy Finished Workshop9test in 0:00:06.674509

All sub-tests

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{"tests": {"C001_Carbohydrates_Demo01": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nPDB file name: alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp\nTotal residues: 3\nSequence: ZZZ\nFold tree:\nFOLD_TREE EDGE 1 3 -1 \nPDB file name: alpha-D-Glcp-(1->6)-alpha-D-Glcp\nTotal residues: 2\nSequence: ZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 \nPDB file name: beta-D-Galp-(1->4)-alpha-D-Glcp\nTotal residues: 2\nSequence: ZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 \nalpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp\nalpha-D-Glcp-(1->6)-alpha-D-Glcp\nbeta-D-Galp-(1->4)-alpha-D-Glcp\n1 ->4)-alpha-D-Glcp:reducing_end\n2 ->4)-beta-D-Galp:non-reducing_end\n1 ->4)-alpha-D-Glcp:reducing_end\n2 ->4)-alpha-D-Glcp\n3 ->4)-alpha-D-Glcp:non-reducing_end\nResidue 1: ->4)-alpha-D-Glcp:reducing_end:non-reducing_end (Glc, Z):\nBase: ->4)-alpha-D-Glcp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: glucose\n IUPAC Name: alpha-D-glucopyranose\n Abbreviation: alpha-D-Glcp\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n none\n Polymeric Information:\n Reducing?: yes\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : axial\n O2 : equatorial\n O3 : equatorial\n O4 : equatorial\n C6 : equatorial\nAtom Coordinates:\n C1 : 0, 0, 0\n C2 : 1.55, 0, 0\n C3 : 2.04812, 1.44664, 0\n C4 : 1.50806, 2.11919, -1.26369\n O4 : 1.94666, 3.46908, -1.30661\n C5 : -0.0200415, 2.06186, -1.21358\n O5 : -0.475077, 0.686176, -1.1593\n VO5: -0.492509, 0.676579, -1.17187 (virtual)\n VC1: 0.031762, 0.00822503, 0.00564973 (virtual)\n O1 : -0.494034, 0.697555, 1.2082\n O2 : 2.02401, -0.669275, 1.15922\n O3 : 3.4779, 1.4716, 1.64563e-16\n C6 : -0.614146, 2.71298, -2.43962\n O6 : -0.225074, 4.07556, -2.53127\n H1 : -0.370662, -1.03564, 0.00767336\n H2 : 1.90812, -0.520035, -0.900727\n H3 : 1.67301, 1.95456, 0.900727\n H4 : 1.88381, 1.57916, -2.14527\n HO4: 1.61609, 3.94572, -0.516717\n H5 : -0.369153, 2.59396, -0.316372\n HO1: -0.167832, 1.62167, 1.20877\n HO2: 3.00401, -0.669275, 1.15922\n HO3: 3.78886, 2.40096, 5.03844e-17\n 1H6 : -1.71106, 2.65811, -2.3783\n 2H6 : -0.261365, 2.17983, -3.33478\n HO6: -0.621924, 4.47587, -3.33293\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 1: ->4)-alpha-D-Galp:reducing_end:non-reducing_end (Gal, Z):\nBase: ->4)-alpha-D-Galp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: galactose\n IUPAC Name: alpha-D-galactopyranose\n Abbreviation: alpha-D-Galp\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n none\n Polymeric Information:\n Reducing?: yes\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : axial\n O2 : equatorial\n O3 : equatorial\n O4 : axial\n C6 : equatorial\nAtom Coordinates:\n C1 : 0, 0, 0\n C2 : 1.55, 0, 0\n C3 : 2.04812, 1.44664, 0\n C4 : 1.50806, 2.11919, -1.26369\n O4 : 1.98701, 1.42994, -2.4091\n C5 : -0.0200415, 2.06186, -1.21358\n O5 : -0.475077, 0.686176, -1.1593\n VO5: -0.492509, 0.676579, -1.17187 (virtual)\n VC1: 0.031762, 0.00822503, 0.00564973 (virtual)\n O1 : -0.494034, 0.697555, 1.2082\n O2 : 2.02401, -0.669275, 1.15922\n O3 : 3.4779, 1.4716, 1.64563e-16\n C6 : -0.614146, 2.71298, -2.43962\n O6 : -0.225074, 4.07556, -2.53127\n H1 : -0.370662, -1.03564, 0.00767336\n H2 : 1.90812, -0.520035, -0.900727\n H3 : 1.67301, 1.95456, 0.900727\n H4 : 1.85245, 3.16359, -1.28863\n HO4: 2.96665, 1.45445, -2.41977\n H5 : -0.369153, 2.59396, -0.316372\n HO1: -0.167832, 1.62167, 1.20877\n HO2: 3.00401, -0.669275, 1.15922\n HO3: 3.78886, 2.40096, 5.03844e-17\n 1H6 : -1.71106, 2.65811, -2.3783\n 2H6 : -0.261365, 2.17983, -3.33478\n HO6: -0.621924, 4.47587, -3.33293\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 1: ->3)-alpha-D-Manp:reducing_end:non-reducing_end (Man, Z):\nBase: ->3)-alpha-D-Manp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 O3 \n Backbone atoms: C1 C2 C3 O3 C4 C5 O5 VO5 VC1 H1 H2 H3 HO3 H4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O4 C6 O6 HO1 HO2 HO4 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: mannose\n IUPAC Name: alpha-D-mannopyranose\n Abbreviation: alpha-D-Manp\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n none\n Polymeric Information:\n Reducing?: yes\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : axial\n O2 : axial\n O3 : equatorial\n O4 : equatorial\n C6 : equatorial\nAtom Coordinates:\n C1 : 0, 0, 0\n C2 : 1.55, 0, 0\n C3 : 2.04812, 1.44664, 0\n O3 : 3.4779, 1.4716, 1.64563e-16\n C4 : 1.50806, 2.11919, -1.26369\n C5 : -0.0200415, 2.06186, -1.21358\n O5 : -0.475077, 0.686176, -1.1593\n VO5: -0.492509, 0.676579, -1.17187 (virtual)\n VC1: 0.031762, 0.00822503, 0.00564973 (virtual)\n O1 : -0.494034, 0.697555, 1.2082\n O2 : 2.02401, -0.669275, -1.15922\n O4 : 1.94666, 3.46908, -1.30661\n C6 : -0.614146, 2.71298, -2.43962\n O6 : -0.225074, 4.07556, -2.53127\n H1 : -0.370662, -1.03564, 0.00767336\n H2 : 1.90812, -0.520035, 0.900727\n H3 : 1.67301, 1.95456, 0.900727\n HO3: 3.78886, 2.40096, 5.03844e-17\n H4 : 1.88381, 1.57916, -2.14527\n H5 : -0.369153, 2.59396, -0.316372\n HO1: -0.167832, 1.62167, 1.20877\n HO2: 3.00401, -0.669275, -1.15922\n HO4: 1.61609, 3.94572, -0.516717\n 1H6 : -1.71106, 2.65811, -2.3783\n 2H6 : -0.261365, 2.17983, -3.33478\n HO6: -0.621924, 4.47587, -3.33293\nMirrored relative to coordinates in ResidueType: FALSE\n\n59.99999999999999\n-59.99999999999999\n60.00000000000001\n-59.999999999999986\n59.99999999999999\n4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\nPDB file name: ../test/data/carbohydrates/Lex.pdb\nTotal residues: 3\nSequence: ZZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 EDGE 1 3 -2 O3 C1 \nbeta-D-Galp-(1->4)-beta-D-GlcpNAc\nalpha-L-Fucp-\nResidue 1: ->4)-beta-D-Glcp:reducing_end:->3)-branch:2-AcNH (Glc, Z):\nBase: ->4)-beta-D-Glcp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS BRANCH_POINT POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR C2_MODIFIED ACETYLAMINO_SUGAR\n Variant types: LOWER_TERMINUS_VARIANT C3_BRANCH_POINT C2_ACETYLAMINO_SUGAR\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO4 HO3 HO2 N2 CN2 CAN2 OCN2 HO1 1H6 2H6 HO6 HN2 1HC2 2HC2 3HC2\n Branch-point atoms: O3 \nCarbohydrate Properties for this Residue:\n Basic Name: glucosamine\n IUPAC Name: ->4)-beta-2-(N-acetylamino)-2-deoxy-D-glucopyranose\n Abbreviation: ->4)-beta-D-GlcpNAc\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: beta\n Modifications: \n acetylamino sugar\n Polymeric Information:\n Reducing?: yes\n Main chain connection: (_->4)\n Branch connections: (_->3)\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : equatorial\n N2 : equatorial\n O3 : equatorial\n O4 : equatorial\n C6 : equatorial\nAtom Coordinates:\n C1 : 35.71, 122.693, 36.907\n C2 : 36.264, 121.664, 35.887\n C3 : 35.396, 120.362, 35.896\n C4 : 35.215, 119.833, 37.36\n O4 : 34.235, 118.792, 37.37\n C5 : 34.756, 121.002, 38.316\n O5 : 35.66, 122.104, 38.21\n VO5: 35.66, 122.104, 38.21 (virtual)\n VC1: 35.7109, 122.617, 36.8656 (virtual)\n O1 : 36.369, 123.964, 36.94\n O2 : 36.2371, 122.227, 34.5836 (virtual)\n O3 : 36.026, 119.359, 35.094\n C6 : 34.689, 120.7, 39.82\n O6 : 35.928, 120.224, 40.287\n HO4: 34.615, 117.665, 38.155 (virtual)\n HO3: 35.546, 119.238, 33.75 (virtual)\n HO2: 36.5871, 121.577, 33.9392 (virtual)\n N2 : 36.245, 122.328, 34.583\n CN2: 37.363, 122.3, 33.878\n CAN2: 37.043, 123.112, 32.473\n OCN2: 38.517, 122.472, 34.271\n H1 : 34.6514, 122.845, 36.6496\n H2 : 37.299, 121.411, 36.1601\n H3 : 34.408, 120.587, 35.4681\n H4 : 36.1743, 119.429, 37.7162\n H5 : 33.7421, 121.32, 38.0316\n HO1: 36.301, 124.391, 36.0604\n 1H6 : 33.9192, 119.935, 39.9976\n 2H6 : 34.4315, 121.623, 40.3596\n HO6: 35.8659, 120.037, 41.247\n HN2: 35.4316, 122.782, 34.2477\n 1HC2: 36.3241, 123.919, 32.671\n 2HC2: 36.5729, 122.428, 31.7525\n 3HC2: 37.9836, 123.478, 32.0377\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 2: ->4)-beta-D-Galp:non-reducing_end (Gal, Z):\nBase: ->4)-beta-D-Galp\n Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: galactose\n IUPAC Name: beta-D-galactopyranosyl\n Abbreviation: beta-D-Galp-\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: beta\n Modifications: \n none\n Polymeric Information:\n Reducing?: no\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O2 : equatorial\n O3 : equatorial\n O4 : axial\n C6 : equatorial\nAtom Coordinates:\n C1 : 34.615, 117.665, 38.155\n C2 : 33.365, 116.921, 38.692\n C3 : 33.836, 115.668, 39.463\n C4 : 34.765, 114.785, 38.592\n O4 : 33.936, 114.234, 37.591\n C5 : 35.931, 115.629, 38.011\n O5 : 35.406, 116.786, 37.348\n VO5: 35.406, 116.786, 37.348 (virtual)\n VC1: 34.6528, 117.616, 38.2521 (virtual)\n O1 : 34.235, 118.792, 37.37 (virtual)\n O2 : 32.626, 117.74, 39.575\n O3 : 32.706, 114.881, 39.893\n C6 : 36.818, 114.855, 37.032\n O6 : 37.611, 113.891, 37.692\n HO1: 35.215, 119.833, 37.36 (virtual)\n H1 : 35.2209, 118.009, 39.0061\n H2 : 32.7301, 116.628, 37.8427\n H3 : 34.3885, 115.986, 40.3595\n H4 : 35.1785, 113.978, 39.2143\n HO4: 33.2273, 113.702, 38.0094\n H5 : 36.5692, 115.975, 38.8375\n HO2: 31.8431, 117.248, 39.8996\n HO3: 33.0232, 114.092, 40.3795\n 1H6 : 37.4842, 115.562, 36.5164\n 2H6 : 36.1787, 114.34, 36.2998\n HO6: 38.1635, 113.417, 37.0358\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 3: ->4)-alpha-L-Fucp:non-reducing_end (Fuc, Z):\nBase: ->4)-alpha-L-Fucp\n Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE L_SUGAR PYRANOSE ALPHA_SUGAR C6_MODIFIED DEOXY_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT C6_DEOXY_SUGAR\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO6 HO2 HO3 1H6 2H6 3H6 \nCarbohydrate Properties for this Residue:\n Basic Name: fucose\n IUPAC Name: alpha-L-fucopyranosyl\n Abbreviation: alpha-L-Fucp-\n Classification: aldohexose\n Stereochemistry: L\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n deoxy sugar\n Polymeric Information:\n Reducing?: no\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 1C4 (chair): C-P parameters (q, phi, theta): 0.55, 180, 180; nu angles (degrees): -60, 60, -60, 60, -60, 60\n O2 : equatorial\n O3 : equatorial\n O4 : axial\n C6 : equatorial\nAtom Coordinates:\n C1 : 35.546, 119.238, 33.75\n C2 : 36.615, 118.464, 32.939\n C3 : 36.681, 116.991, 33.421\n C4 : 35.284, 116.331, 33.366\n O4 : 34.915, 116.247, 31.999\n C5 : 34.24, 117.183, 34.142\n O5 : 34.28, 118.546, 33.673\n VO5: 34.28, 118.546, 33.673 (virtual)\n VC1: 35.5799, 119.134, 33.8691 (virtual)\n O1 : 36.026, 119.359, 35.094 (virtual)\n O2 : 37.839, 119.137, 33.073\n O3 : 37.527, 116.202, 32.617\n C6 : 32.809, 116.64, 34.044\n O6 : 32.372, 116.598, 32.6936 (virtual)\n HO1: 35.396, 120.362, 35.896 (virtual)\n HO6: 31.4572, 116.249, 32.6565 (virtual)\n H1 : 35.3955, 120.244, 33.3315\n H2 : 36.3437, 118.489, 31.8733\n H3 : 37.0471, 116.97, 34.4581\n H4 : 35.3419, 115.332, 33.8218\n HO4: 34.8869, 117.147, 31.6118\n H5 : 34.5158, 117.205, 35.2067\n HO2: 38.5305, 118.662, 32.5661\n HO3: 37.538, 115.283, 32.9572\n 1H6 : 32.7831, 115.622, 34.4596\n 2H6 : 32.137, 117.296, 34.6166\n 3H6 : 32.5045, 116.622, 32.9871\nMirrored relative to coordinates in ResidueType: FALSE\n\nPDB file name: ../test/data/carbohydrates/N-linked_14-mer_glycan.pdb\nTotal residues: 19\nSequence: ANASAZZZZZZZZZZZZZZ\nFold tree:\nFOLD_TREE EDGE 1 5 -1 EDGE 2 6 -2 ND2 C1 EDGE 6 14 -1 EDGE 8 15 -2 O6 C1 EDGE 15 17 -1 EDGE 15 18 -2 O6 C1 EDGE 18 19 -1 \nANASA\nalpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-beta-D-GlcpNAc-\nalpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-alpha-D-Manp-\nalpha-D-Manp-(1->2)-alpha-D-Manp-\nPDB file name: ../test/data/carbohydrates/O_glycan.pdb\nTotal residues: 4\nSequence: ASAZ\nFold tree:\nFOLD_TREE EDGE 1 3 -1 EDGE 2 4 -2 OG C1 \nASA\nalpha-D-Glcp-\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -constant_seed -include_sugars -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.73307 seconds.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/maltotriose.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/isomaltose.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.Conformation: appending residue by a chemical bond in the foldtree: 3 ->4)-alpha-L-Fucp:non-reducing_end anchor: O3 1 root: C1 \ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/Lex.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Gal2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Fuc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 3 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/N-linked_14-mer_glycan.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc6 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc7 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man8 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man9 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man10 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man11 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc12 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc13 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc14 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man15 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man16 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man17 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man18 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man19 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 6 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 15 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 18 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/O_glycan.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc4 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 4 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->4)-alpha-D-Glcp:non-reducing_end anchor: OG 2 root: C1 \ncore.pose.carbohydrates.util: Glycosylated pose with a(n) Glcp-OGSER2 bond.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose.carbohydrates.util: Idealizing glycosidic torsions.\ncore.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->3)-alpha-D-Galp:2-AcNH anchor: OG 2 root: C1 \ncore.pose.carbohydrates.util: Glycosylated pose with a(n) a-D-GalpNAc-(1->3)-a-D-GalpNAc--OGSER2 bond.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose.carbohydrates.util: Idealizing glycosidic torsions.\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.core.pose import pose_from_saccharide_sequence\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:42: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for res in lactose: print( res.seqpos(), res.name() )\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:43: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for res in maltotriose: print( res.seqpos(), res.name() )\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/C001_Carbohydrates_Demo01.py:128: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for res in Lex: print( res )\n\nFinished C001_Carbohydrates_Demo01 in 0:00:18.601279", "state": "passed"}, "D010_Pose_structure": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\n================================================================================\nLoaded from ../test/data/test_in.pdb\n116 residues\n1 chain(s) ('A')\nSequence:\nDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL\nSecondary Structure:\nLHHHHHHHHHHHHLLLLLLLLLHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHLLLLLLLLLLLLLL\n\t63.7% Helical\n\t0.0% Sheet\n\t36.2% Loop\n================================================================================\nPose numbered Residue 58\nPDB numbered Residue 58\nSingle Letter: T\nChain: A\nSecondary Structure: Helix\nPhi: -66.10647574201569\nPsi: -37.61278973721056\nOmega: 179.8787072171539\nChi 1: 157.77746590432227\nChi 2: 179.99312165369778\n================================================================================\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.989654 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nprotocols.DsspMover: LHHHHHHHHHHHHLLLLLLLLLHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHLLLLLLLLLLLLLL\n\nFinished D010_Pose_structure in 0:00:17.277707", "state": "passed"}, "D020_Pose_scoring": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n================================================================================\nScoreFunction a: 949.3120641217009\nScoreFunction b: 949.3120641217009\nScoreFunction c: 54.59531500722412\nScoreFunction d: 54.59531500722412\nScoreFunction e: 639.6921382070861\n================================================================================\nLoaded from ../test/data/test_in.pdb\n116 residues\nRadius of Gyration ~ 15.070968422880075\nTotal Rosetta Score: 639.6921382070861\n================================================================================\nPose numbered Residue 58\nTotal Residue Score: 17.835676002501444\nScore Breakdown:\n---------------------------------------------\n\tfa_atr :\t -6.767255537709819\n\tfa_rep :\t 18.770496833063742\n\tfa_sol :\t 4.234940603509646\n\tfa_intra_rep :\t 0.0152272562193792\n\tfa_elec :\t -1.0892415802359439\n\tpro_close :\t 0.0\n\thbond_sr_bb :\t 0.0\n\thbond_lr_bb :\t 0.0\n\thbond_bb_sc :\t 0.0\n\thbond_sc :\t 0.0\n\tdslf_fa13 :\t 0.0\n\trama :\t -0.13507819308968252\n\tomega :\t -0.006962209630289949\n\tfa_dun :\t 3.0402048792529506\n\tp_aa_pp :\t 0.043343951121461305\n\tref :\t -0.27\n---------------------------------------------\nHydrogen bonds involving Residue 58:\n58 H => 54 O |score: -0.9409534230157675\n62 H => 58 O |score: -0.7406209609222881\n================================================================================\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.9625 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.276951 seconds to load from binary\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.800 -715.300 -572.240\n fa_rep 0.440 827.739 364.205\n fa_sol 0.750 504.855 378.642\n fa_intra_rep 0.004 563.466 2.254\n fa_elec 0.700 -133.742 -93.619\n pro_close 1.000 17.220 17.220\n hbond_sr_bb 1.170 -47.398 -55.455\n hbond_lr_bb 1.170 -0.785 -0.918\n hbond_bb_sc 1.170 -5.673 -6.637\n hbond_sc 1.100 -1.540 -1.693\n dslf_fa13 1.000 0.000 0.000\n rama 0.200 4.872 0.974\n omega 0.500 16.053 8.026\n fa_dun 0.560 1133.922 634.996\n p_aa_pp 0.320 -17.819 -5.702\n ref 1.000 -30.360 -30.360\n---------------------------------------------------\n Total weighted score: 639.692\n\nFinished D020_Pose_scoring in 0:00:19.981126", "state": "passed"}, "D030_Fold_tree": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\nThe first FoldTree is proper: True\nThe second FoldTree is proper: True\n\nlinearized structure output\npre jump perturbed structure output\nfirst internal jump edge perturbed structure output\nsecond internal jump edge perturbed structure output\npost jump perturbed structure output\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.05345 seconds.\n\nFinished D030_Fold_tree in 0:00:17.101115", "state": "passed"}, "D040_Movemap": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.08629 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n resnum BB CHI NU BRANCH\n 001 TRUE FALSE FALSE FALSE\n 002 TRUE FALSE FALSE FALSE\n 003 TRUE FALSE FALSE FALSE\n 004 TRUE FALSE FALSE FALSE\n 005 TRUE FALSE FALSE FALSE\n 006 TRUE FALSE FALSE FALSE\n 007 TRUE FALSE FALSE FALSE\n 008 TRUE FALSE FALSE FALSE\n 009 TRUE FALSE FALSE FALSE\n 010 TRUE FALSE FALSE FALSE\n 011 TRUE FALSE FALSE FALSE\n 012 TRUE FALSE FALSE FALSE\n 013 TRUE FALSE FALSE FALSE\n 014 TRUE FALSE FALSE FALSE\n 015 TRUE FALSE FALSE FALSE\n 016 TRUE FALSE FALSE FALSE\n 017 TRUE FALSE FALSE FALSE\n 018 TRUE FALSE FALSE FALSE\n 019 TRUE FALSE FALSE FALSE\n 020 TRUE FALSE FALSE FALSE\n 021 TRUE FALSE FALSE FALSE\n 022 TRUE FALSE FALSE FALSE\n 023 TRUE FALSE FALSE FALSE\n 024 TRUE FALSE FALSE FALSE\n 025 TRUE FALSE FALSE FALSE\n 026 TRUE FALSE FALSE FALSE\n 027 TRUE FALSE FALSE FALSE\n 028 TRUE FALSE FALSE FALSE\n 029 TRUE FALSE FALSE FALSE\n 030 TRUE FALSE FALSE FALSE\n 031 TRUE FALSE FALSE FALSE\n 032 TRUE FALSE FALSE FALSE\n 033 TRUE FALSE FALSE FALSE\n 034 TRUE FALSE FALSE FALSE\n 035 TRUE FALSE FALSE FALSE\n 036 TRUE FALSE FALSE FALSE\n 037 TRUE FALSE FALSE FALSE\n 038 TRUE FALSE FALSE FALSE\n 039 TRUE FALSE FALSE FALSE\n 040 TRUE FALSE FALSE FALSE\n 041 TRUE FALSE FALSE FALSE\n 042 TRUE FALSE FALSE FALSE\n 043 TRUE FALSE FALSE FALSE\n 044 TRUE FALSE FALSE FALSE\n 045 TRUE FALSE FALSE FALSE\n 046 TRUE FALSE FALSE FALSE\n 047 TRUE FALSE FALSE FALSE\n 048 TRUE FALSE FALSE FALSE\n 049 TRUE FALSE FALSE FALSE\n 050 TRUE FALSE FALSE FALSE\n 051 TRUE FALSE FALSE FALSE\n 052 TRUE FALSE FALSE FALSE\n 053 TRUE FALSE FALSE FALSE\n 054 TRUE FALSE FALSE FALSE\n 055 TRUE FALSE FALSE FALSE\n 056 TRUE FALSE FALSE FALSE\n 057 TRUE FALSE FALSE FALSE\n 058 TRUE FALSE FALSE FALSE\n 059 TRUE FALSE FALSE FALSE\n 060 TRUE FALSE FALSE FALSE\n 061 TRUE FALSE FALSE FALSE\n 062 TRUE FALSE FALSE FALSE\n 063 TRUE FALSE FALSE FALSE\n 064 TRUE FALSE FALSE FALSE\n 065 TRUE FALSE FALSE FALSE\n 066 TRUE FALSE FALSE FALSE\n 067 TRUE FALSE FALSE FALSE\n 068 TRUE FALSE FALSE FALSE\n 069 TRUE FALSE FALSE FALSE\n 070 TRUE FALSE FALSE FALSE\n 071 TRUE FALSE FALSE FALSE\n 072 TRUE FALSE FALSE FALSE\n 073 TRUE FALSE FALSE FALSE\n 074 TRUE FALSE FALSE FALSE\n 075 TRUE FALSE FALSE FALSE\n 076 TRUE FALSE FALSE FALSE\n 077 TRUE FALSE FALSE FALSE\n 078 TRUE FALSE FALSE FALSE\n 079 TRUE FALSE FALSE FALSE\n 080 TRUE FALSE FALSE FALSE\n 081 TRUE FALSE FALSE FALSE\n 082 TRUE FALSE FALSE FALSE\n 083 TRUE FALSE FALSE FALSE\n 084 TRUE FALSE FALSE FALSE\n 085 TRUE FALSE FALSE FALSE\n 086 TRUE FALSE FALSE FALSE\n 087 TRUE FALSE FALSE FALSE\n 088 TRUE FALSE FALSE FALSE\n 089 TRUE FALSE FALSE FALSE\n 090 TRUE FALSE FALSE FALSE\n 091 TRUE FALSE FALSE FALSE\n 092 TRUE FALSE FALSE FALSE\n 093 TRUE FALSE FALSE FALSE\n 094 TRUE FALSE FALSE FALSE\n 095 TRUE FALSE FALSE FALSE\n 096 TRUE FALSE FALSE FALSE\n 097 TRUE FALSE FALSE FALSE\n 098 TRUE FALSE FALSE FALSE\n 099 TRUE FALSE FALSE FALSE\n 100 TRUE FALSE FALSE FALSE\n 101 TRUE FALSE FALSE FALSE\n 102 TRUE FALSE FALSE FALSE\n 103 TRUE FALSE FALSE FALSE\n 104 TRUE FALSE FALSE FALSE\n 105 TRUE FALSE FALSE FALSE\n 106 TRUE FALSE FALSE FALSE\n 107 TRUE FALSE FALSE FALSE\n 108 TRUE FALSE FALSE FALSE\n 109 TRUE FALSE FALSE FALSE\n 110 TRUE FALSE FALSE FALSE\n 111 TRUE FALSE FALSE FALSE\n 112 TRUE FALSE FALSE FALSE\n 113 TRUE FALSE FALSE FALSE\n 114 TRUE FALSE FALSE FALSE\n 115 TRUE FALSE FALSE FALSE\n 116 TRUE FALSE FALSE FALSE\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\nPre minimization score: 949.3120641217009\nPost minimization score: 699.8780157437467\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.271517 seconds to load from binary\n\nFinished D040_Movemap in 0:00:21.149679", "state": "passed"}, "D050_Packer_task": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tASP:NtermProteinFull\n2\tTRUE\tFALSE\tALA\n3\tTRUE\tFALSE\tILE\n4\tTRUE\tFALSE\tTHR\n5\tTRUE\tFALSE\tILE\n6\tTRUE\tFALSE\tHIS,HIS_D\n7\tTRUE\tFALSE\tSER\n8\tTRUE\tFALSE\tILE\n9\tTRUE\tFALSE\tLEU\n10\tTRUE\tFALSE\tASP\n11\tTRUE\tFALSE\tTRP\n12\tTRUE\tFALSE\tILE\n13\tTRUE\tFALSE\tGLU\n14\tTRUE\tFALSE\tASP\n15\tTRUE\tFALSE\tASN\n16\tTRUE\tFALSE\tLEU\n17\tTRUE\tFALSE\tGLU\n18\tTRUE\tFALSE\tSER\n19\tTRUE\tFALSE\tPRO\n20\tTRUE\tFALSE\tLEU\n21\tTRUE\tFALSE\tSER\n22\tTRUE\tFALSE\tLEU\n23\tTRUE\tFALSE\tGLU\n24\tTRUE\tFALSE\tLYS\n25\tTRUE\tFALSE\tVAL\n26\tTRUE\tFALSE\tSER\n27\tTRUE\tFALSE\tGLU\n28\tTRUE\tFALSE\tARG\n29\tTRUE\tFALSE\tSER\n30\tTRUE\tFALSE\tGLY\n31\tTRUE\tFALSE\tTYR\n32\tTRUE\tFALSE\tSER\n33\tTRUE\tFALSE\tLYS\n34\tTRUE\tFALSE\tTRP\n35\tTRUE\tFALSE\tHIS,HIS_D\n36\tTRUE\tFALSE\tLEU\n37\tTRUE\tFALSE\tGLN\n38\tTRUE\tFALSE\tARG\n39\tTRUE\tFALSE\tMET\n40\tTRUE\tFALSE\tPHE\n41\tTRUE\tFALSE\tLYS\n42\tTRUE\tFALSE\tLYS\n43\tTRUE\tFALSE\tGLU\n44\tTRUE\tFALSE\tTHR\n45\tTRUE\tFALSE\tGLY\n46\tTRUE\tFALSE\tHIS,HIS_D\n47\tTRUE\tFALSE\tSER\n48\tTRUE\tFALSE\tLEU\n49\tTRUE\tFALSE\tGLY\n50\tTRUE\tFALSE\tGLN\n51\tTRUE\tFALSE\tTYR\n52\tTRUE\tFALSE\tILE\n53\tTRUE\tFALSE\tARG\n54\tTRUE\tFALSE\tSER\n55\tTRUE\tFALSE\tARG\n56\tTRUE\tFALSE\tLYS\n57\tTRUE\tFALSE\tMET\n58\tTRUE\tFALSE\tTHR\n59\tTRUE\tFALSE\tGLU\n60\tTRUE\tFALSE\tILE\n61\tTRUE\tFALSE\tALA\n62\tTRUE\tFALSE\tGLN\n63\tTRUE\tFALSE\tLYS\n64\tTRUE\tFALSE\tLEU\n65\tTRUE\tFALSE\tLYS\n66\tTRUE\tFALSE\tGLU\n67\tTRUE\tFALSE\tSER\n68\tTRUE\tFALSE\tASN\n69\tTRUE\tFALSE\tGLU\n70\tTRUE\tFALSE\tPRO\n71\tTRUE\tFALSE\tILE\n72\tTRUE\tFALSE\tLEU\n73\tTRUE\tFALSE\tTYR\n74\tTRUE\tFALSE\tLEU\n75\tTRUE\tFALSE\tALA\n76\tTRUE\tFALSE\tGLU\n77\tTRUE\tFALSE\tARG\n78\tTRUE\tFALSE\tTYR\n79\tTRUE\tFALSE\tGLY\n80\tTRUE\tFALSE\tPHE\n81\tTRUE\tFALSE\tGLU\n82\tTRUE\tFALSE\tSER\n83\tTRUE\tFALSE\tGLN\n84\tTRUE\tFALSE\tGLN\n85\tTRUE\tFALSE\tTHR\n86\tTRUE\tFALSE\tLEU\n87\tTRUE\tFALSE\tTHR\n88\tTRUE\tFALSE\tARG\n89\tTRUE\tFALSE\tTHR\n90\tTRUE\tFALSE\tPHE\n91\tTRUE\tFALSE\tLYS\n92\tTRUE\tFALSE\tASN\n93\tTRUE\tFALSE\tTYR\n94\tTRUE\tFALSE\tPHE\n95\tTRUE\tFALSE\tASP\n96\tTRUE\tFALSE\tVAL\n97\tTRUE\tFALSE\tPRO\n98\tTRUE\tFALSE\tPRO\n99\tTRUE\tFALSE\tHIS,HIS_D\n100\tTRUE\tFALSE\tLYS\n101\tTRUE\tFALSE\tTYR\n102\tTRUE\tFALSE\tARG\n103\tTRUE\tFALSE\tMET\n104\tTRUE\tFALSE\tTHR\n105\tTRUE\tFALSE\tASN\n106\tTRUE\tFALSE\tMET\n107\tTRUE\tFALSE\tGLN\n108\tTRUE\tFALSE\tGLY\n109\tTRUE\tFALSE\tGLU\n110\tTRUE\tFALSE\tSER\n111\tTRUE\tFALSE\tARG\n112\tTRUE\tFALSE\tPHE\n113\tTRUE\tFALSE\tLEU\n114\tTRUE\tFALSE\tHIS,HIS_D\n115\tTRUE\tFALSE\tPRO\n116\tTRUE\tFALSE\tLEU:CtermProteinFull\n\n\nPre packing score: 949.3120641217009\nPost packing score: 119.97075192647779\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tFALSE\tFALSE\t\n2\tFALSE\tFALSE\t\n3\tFALSE\tFALSE\t\n4\tFALSE\tFALSE\t\n5\tFALSE\tFALSE\t\n6\tFALSE\tFALSE\t\n7\tFALSE\tFALSE\t\n8\tFALSE\tFALSE\t\n9\tFALSE\tFALSE\t\n10\tFALSE\tFALSE\t\n11\tFALSE\tFALSE\t\n12\tFALSE\tFALSE\t\n13\tFALSE\tFALSE\t\n14\tFALSE\tFALSE\t\n15\tFALSE\tFALSE\t\n16\tFALSE\tFALSE\t\n17\tFALSE\tFALSE\t\n18\tFALSE\tFALSE\t\n19\tFALSE\tFALSE\t\n20\tFALSE\tFALSE\t\n21\tFALSE\tFALSE\t\n22\tFALSE\tFALSE\t\n23\tFALSE\tFALSE\t\n24\tFALSE\tFALSE\t\n25\tFALSE\tFALSE\t\n26\tFALSE\tFALSE\t\n27\tFALSE\tFALSE\t\n28\tFALSE\tFALSE\t\n29\tFALSE\tFALSE\t\n30\tFALSE\tFALSE\t\n31\tFALSE\tFALSE\t\n32\tFALSE\tFALSE\t\n33\tFALSE\tFALSE\t\n34\tFALSE\tFALSE\t\n35\tFALSE\tFALSE\t\n36\tFALSE\tFALSE\t\n37\tFALSE\tFALSE\t\n38\tFALSE\tFALSE\t\n39\tFALSE\tFALSE\t\n40\tFALSE\tFALSE\t\n41\tFALSE\tFALSE\t\n42\tFALSE\tFALSE\t\n43\tFALSE\tFALSE\t\n44\tFALSE\tFALSE\t\n45\tFALSE\tFALSE\t\n46\tFALSE\tFALSE\t\n47\tFALSE\tFALSE\t\n48\tFALSE\tFALSE\t\n49\tFALSE\tFALSE\t\n50\tFALSE\tFALSE\t\n51\tFALSE\tFALSE\t\n52\tFALSE\tFALSE\t\n53\tFALSE\tFALSE\t\n54\tFALSE\tFALSE\t\n55\tFALSE\tFALSE\t\n56\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n57\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n58\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n59\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n60\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n61\tFALSE\tFALSE\t\n62\tFALSE\tFALSE\t\n63\tFALSE\tFALSE\t\n64\tFALSE\tFALSE\t\n65\tFALSE\tFALSE\t\n66\tFALSE\tFALSE\t\n67\tFALSE\tFALSE\t\n68\tFALSE\tFALSE\t\n69\tFALSE\tFALSE\t\n70\tFALSE\tFALSE\t\n71\tFALSE\tFALSE\t\n72\tFALSE\tFALSE\t\n73\tFALSE\tFALSE\t\n74\tFALSE\tFALSE\t\n75\tFALSE\tFALSE\t\n76\tFALSE\tFALSE\t\n77\tFALSE\tFALSE\t\n78\tFALSE\tFALSE\t\n79\tFALSE\tFALSE\t\n80\tFALSE\tFALSE\t\n81\tFALSE\tFALSE\t\n82\tFALSE\tFALSE\t\n83\tFALSE\tFALSE\t\n84\tFALSE\tFALSE\t\n85\tFALSE\tFALSE\t\n86\tFALSE\tFALSE\t\n87\tFALSE\tFALSE\t\n88\tFALSE\tFALSE\t\n89\tFALSE\tFALSE\t\n90\tFALSE\tFALSE\t\n91\tFALSE\tFALSE\t\n92\tFALSE\tFALSE\t\n93\tFALSE\tFALSE\t\n94\tFALSE\tFALSE\t\n95\tFALSE\tFALSE\t\n96\tFALSE\tFALSE\t\n97\tFALSE\tFALSE\t\n98\tFALSE\tFALSE\t\n99\tFALSE\tFALSE\t\n100\tFALSE\tFALSE\t\n101\tFALSE\tFALSE\t\n102\tFALSE\tFALSE\t\n103\tFALSE\tFALSE\t\n104\tFALSE\tFALSE\t\n105\tFALSE\tFALSE\t\n106\tFALSE\tFALSE\t\n107\tFALSE\tFALSE\t\n108\tFALSE\tFALSE\t\n109\tFALSE\tFALSE\t\n110\tFALSE\tFALSE\t\n111\tFALSE\tFALSE\t\n112\tFALSE\tFALSE\t\n113\tFALSE\tFALSE\t\n114\tFALSE\tFALSE\t\n115\tFALSE\tFALSE\t\n116\tFALSE\tFALSE\t\n\n\nDesign with all proteogenic amino acids at (pose numbered) residues 56 to 60\nPre-design score: 949.3120641217009\nPre-design sequence: ...SRKMTEIAQ...\n\nPost-design score: 880.7910264455371\nPost-design sequence: ...SRIATEIAQ...\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.0745 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.223287 seconds to load from binary\ncore.pack.pack_rotamers: built 3014 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1684 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\n\nFinished D050_Packer_task in 0:00:24.779935", "state": "passed"}, "D060_Folding": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nWorking on decoy: fold_output_0.pdb\n================================================================================\nPotential Disulfides:\n================================================================================\n===== Centroid Scores =====\nOriginal Score\t:\t 445.27957490489933\nfold_output_1 \t:\t 131.88750967868828\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.995886 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.029318 seconds.\ncore.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.245219 seconds to load from binary\n\nFinished D060_Folding in 0:00:21.158163", "state": "passed"}, "D070_Refinement": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nWorking on decoy: refine_output_0.pdb\nOriginal Score\t:\t 949.3120641217009\nrefine_output_1\t:\t -161.54772503563524\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.932208 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.283477 seconds to load from binary\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.pack_rotamers: built 3108 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3310 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3312 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3206 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3281 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3262 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3252 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3292 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 3375 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished D070_Refinement in 0:00:50.150681", "state": "passed"}, "D080_Loop_modeling": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -run:jran 1111125 -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111125 seed_offset=0 real_seed=1111125\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111125 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.945388 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nprotocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 14 -1 EDGE 14 17 -1 EDGE 14 20 1 EDGE 20 18 -1 EDGE 20 116 -1 \nprotocols.loops.loops_main: Added cutpoint variant to residue 17\nprotocols.loops.loops_main: Added cutpoint variant to residue 18\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.029018 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.286346 seconds to load from binary\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.pack_rotamers: built 1795 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loops_main: Added cutpoint variant to residue 17\nprotocols.loops.loops_main: Added cutpoint variant to residue 18\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 825 rotamers at 28 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 138.566 138.566\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 1 138.566\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5737 74.5737\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 70.5721 70.5721\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.7059 62.7059\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.0896 61.0896\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 59.9574 59.9574\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 59.7899 59.7899\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 56.1949 56.1949\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.878 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9522 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9578 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.0426 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 57.9858 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 56.0656 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.6881 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.0689 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.1019 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9445 54.878\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.8568 54.8568\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.2267 54.8568\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.8908 54.8568\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 783 rotamers at 25 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.3263 54.3263\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 2 62.6631\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.5112 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8803 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8753 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9224 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8885 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8894 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8576 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9176 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.7747 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5236 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9741 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9114 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8428 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8527 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5602 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5602 61.5112\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 796 rotamers at 25 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.3972 61.3972\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 3 66.3631\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 66.3631 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 66.3631 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 66.3631 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3767 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4066 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3734 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3549 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3995 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.7208 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.6825 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4082 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3799 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4224 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.365 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3398 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.4835 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.2987 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3489 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.3349 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.2569 66.3631\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 795 rotamers at 25 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 65.9596 65.9596\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 4 69.5649\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 69.5649 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.2748 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3856 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.58 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3005 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3036 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3259 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.4736 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.2659 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.2677 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.3206 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.291 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.4704 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 72.268 69.5649\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 794 rotamers at 25 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 68.7119 68.7119\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 5 71.0257\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 71.0257 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 71.0257 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.7812 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5137 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5396 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5293 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5465 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5153 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5033 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.4984 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5009 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5585 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefin\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nWorking on decoy: loop_output_0.pdb\neInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5506 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5025 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5046 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5405 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.7434 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5965 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5456 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5932 71.0257\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 794 rotamers at 25 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 71.4655 71.0257\nprotocols.moves.TrialCounter: repack trials= 6; accepts= 1.0000; energy_drop/trial= -2.36900\nprotocols.moves.TrialCounter: shear_ccd_min trials= 50; accepts= 0.8400; energy_drop/trial= 0.09451\nprotocols.moves.TrialCounter: small_ccd_min trials= 50; accepts= 0.8200; energy_drop/trial= -1.58677\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/demo/D080_Loop_modeling.py:131: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.loops.loop_mover.refine import LoopMover_Refine_CCD\n\nFinished D080_Loop_modeling in 0:01:05.203697", "state": "passed"}, "D090_Ala_scan": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.05159 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.276329 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 180 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 189 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 176 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 185 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 463 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 481 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 374 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 392 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 253 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 288 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 222 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 244 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 0 rotamers at 0 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 382 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 403 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 382 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 403 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 761 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 769 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 761 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 769 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 661 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 701 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 583 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 623 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 0 rotamers at 0 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 479 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 487 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 479 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 487 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 450 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 477 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 442 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 469 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 400 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 422 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 494 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 516 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 193 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 217 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 165 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 189 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 115 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 123 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 62 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 70 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 184 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 185 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 160 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 160 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 152 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 175 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 86 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 109 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 694 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 694 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 378 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 378 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 0 rotamers at 0 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 451 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 476 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 451 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 476 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 271 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 306 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 241 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 262 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 334 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 369 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 388 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 423 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 573 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 598 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 543 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 560 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 837 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 877 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 676 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 716 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 675 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 688 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 453 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 466 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 747 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 747 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 745 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 745 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 643 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 675 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 482 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 514 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 551 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 578 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 514 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 513 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 860 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 916 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 866 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 868 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 819 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 819 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 658 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 658 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 512 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 620 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 405 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 513 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 491 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 491 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 438 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 438 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 457 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 485 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 454 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 482 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 377 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 377 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 373 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 373 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 349 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 295 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 331 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 277 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 430 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 538 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 168 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 276 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 217 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 325 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 164 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 164 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 509 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 638 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 490 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 600 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 289 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 453 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 287 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 451 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 523 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 563 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 416 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 456 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 629 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 723 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 634 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 733 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 460 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 492 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 426 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 450 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 420 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 468 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 414 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 454 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInte\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n================================================================================\nTrial 1\nMutants (PDB numbered)\t\"ddG\" (interaction dependent score change)\nF39A\t0.3037419927867404\nH40A\t0.062291291501423984\nF41A\t-0.5179182491857546\nC42A\t0.0\nA55A\t0.7526408562278846\nH57A\t-1.8773173484200072\nC58A\t-0.2193728458406099\nI99A\t0.8234264858139682\nG142A\t0.010933632634589685\nL143A\t1.3741232149200755\nT151A\t0.43839262942344703\nW172A\t1.0909707675280913\nK175A\t-0.17668088813627492\nS190A\t-0.43304128739850967\nC191A\t0.0\nM192A\t-0.3059494545528878\nG193A\t-1.0066840572941373\nD194A\t0.7375507270811852\nS195A\t-3.072403605789475\nG196A\t-0.656357391887866\nV213A\t0.5586573712038216\nS214A\t-1.1522661010514526\nW215A\t-1.109766942631154\nG216A\t-1.4328724668491475\nS217A\t-0.3300597192764201\nS218A\t-3.1289141356602954\nT219A\t-0.158856433434579\nV227A\t-0.14919286885873362\nL37A\t-0.0781716063218596\nE39A\t-0.2842576324852075\nG40A\t-0.35176205410326133\nS41A\t-0.32954428119910517\nP42A\t1.3097229786820321\nV43A\t1.5310898301999032\nT44A\t-1.7214007763273287\nL45A\t0.8101922525750069\nD46A\t-4.459550972237139\nL47A\t0.7556054312547076\nR48A\t-0.5921687568389871\nY49A\t-1.1555400302177077\nR53A\t-0.02278040179214713\nF55A\t-1.3537481969085547\nG70A\t0.04813369810437962\n================================================================================\nLikely Hotspot Residues\nH57A\nL143A\nW172A\nS195A\nS218A\nP42A\nV43A\nT44A\nD46A\n================================================================================\nractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 179 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 212 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 82 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 113 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 136 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 148 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 127 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 139 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 285 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 285 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 194 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 194 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 407 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 353 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 372 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 318 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 170 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 210 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 188 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 228 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/demo/D090_Ala_scan.py:84: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.scoring import Interface\n\nFinished D090_Ala_scan in 0:00:50.520282", "state": "passed"}, "D100_Docking": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.951995 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.284328 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.029844 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.docking.DockingInitialPerturbation: Reading options...\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.moves.RigidBodyMover: Randomize: Jump (before): RT -0.43256 0.815075 -0.385415 -0.869462 -0.490229 -0.0609182 -0.238594 0.308753 0.92073 -20.1643 -14.8001 1.00855 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (before): 7.27132 -0.353633 18.2062\nprotocols.geometry.RB_geometry: random_reorientation_matrix phi: 99.6306 psi: 274.195 theta: 88.635\nprotocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.501566 0.0943906 -0.859955 -0.450893 -0.819823 -0.352967 -0.738328 0.564784 -0.368635 1.19304 -6.08076 -26.9467 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (after): 7.27132 -0.353633 18.2062\nprotocols.moves.RigidBodyMover: Randomize: ---\nprotocols.moves.RigidBodyMover: Randomize: Jump (before): RT 0.501566 0.0943906 -0.859955 -0.450893 -0.819823 -0.352967 -0.738328 0.564784 -0.368635 1.19304 -6.08076 -26.9467 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (before): 14.3539 25.5364 12.8647\nprotocols.geometry.RB_geometry: random_reorientation_matrix phi: 168.165 psi: 253.962 theta: 126.406\nprotocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.90194 0.265425 -0.340666 0.355013 -0.00652657 0.934839 0.245906 -0.964109 -0.100116 3.28027 -14.8952 32.2801 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (after): 26.3065 0.818941 -13.1763\nprotocols.moves.RigidBodyMover: Randomize: ---\nprotocols.moves.RigidBodyMover: Spin: Jump (before): RT 0.904505 0.256377 -0.340796 0.348103 0.017797 0.937287 0.246364 -0.966413 -0.0731481 7.43102 0.0211541 38.4478 \nprotocols.moves.RigidBodyMover: Spin: Rot (before): 15.2576 -9.26054 -20.5784\nprotocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.96652 0.250828 -0.0540836 0.0814818 -0.10016 0.991629 0.243312 -0.962836 -0.117244 6.83388 -0.112006 38.5401 \nprotocols.moves.RigidBodyMover: Spin: Rot (after): 15.2576 -9.26054 -20.5784\nprotocols.moves.RigidBodyMover: Spin: ---\nprotocols.docking.DockingInitialPerturbation: sliding into contact\nprotocols.docking.DockingInitialPerturbation: Moving away\nprotocols.docking.DockingInitialPerturbation: Moving together\nbasic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score\nprotocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!\nprotocols.docking.DockingProtocol: Setting docking foldtree\nprotocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 \nprotocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 \nprotocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingProtocol: /// Rosetta 3 Docking Protocol ///\nprotocols.docking.DockingProtocol: /// ///\nprotocols.docking.DockingProtocol: /// Dockable Jumps: 1 ///\nprotocols.docking.DockingProtocol: /// Low Resolution Docking Protocol: on ///\nprotocols.docking.DockingProtocol: /// High Resolution Docking Protocol: on ///\nprotocols.docking.DockingProtocol: /// Low Resolution Filter: on ///\nprotocols.docking.DockingProtocol: /// High Resolution Filter: on ///\nprotocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingProtocol: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 \nprotocols.docking.DockingInitialPerturbation: sliding into contact for centroid mode\nprotocols.docking.DockingInitialPerturbation: sliding into contact\nprotocols.docking.DockingInitialPerturbation: Moving away\nprotocols.docking.DockingInitialPerturbation: Moving together\nprotocols.docking.DockingProtocol: finished initial perturbation\nprotocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... \nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.32\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.1\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.1\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.06\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.14\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.04\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.14\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 4 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 8 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 9 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 10 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 11 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 13 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 14 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 15 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 16 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 19 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 20 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 21 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 22 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 24 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 25 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 26 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 27 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 28 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 29 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 30 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 31 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 32 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 33 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 35 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 37 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 38 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 39 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 40 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 43 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 44 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 45 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 46 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 47 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 48 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 49 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 50 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 51 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 52 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 53 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 54 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 55 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 56 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 58 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 59 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 60 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 61 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 62 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 63 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 64 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 66 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 68 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 69 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 70 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 71 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 73 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 74 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 75 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 77 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 78 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 79 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 80 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 81 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 82 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 83 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 85 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 86 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 87 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 88 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 89 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 91 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 92 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 93 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 94 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 95 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 96 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 97 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 98 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 99 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 100 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 101 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 103 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 104 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 105 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 106 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 107 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 108 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 110 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 112 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 114 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 115 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 116 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 117 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 118 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 119 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 120 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 121 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 122 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 123 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 124 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 125 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 126 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 127 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 128 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 129 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 131 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 132 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 133 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 134 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 135 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 136 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 138 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 141 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 143 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 144 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 145 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 146 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 148 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 149 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 150 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 151 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 152 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 153 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 154 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 155 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 156 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 157 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 158 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 159 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 160 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 161 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 165 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 167 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 168 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 169 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 170 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 171 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 172 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 173 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 174 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 175 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 176 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 178 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 179 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 181 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 182 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 183 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 184 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 185 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 187 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 188 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 191 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 192 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 193 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 194 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 195 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 197 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 199 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 200 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 201 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 202 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 203 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 205 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 206 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 207 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 208 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 210 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 211 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 212 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 213 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 215 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 216 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 217 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 218 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 221 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 222 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 223 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 224 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 225 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 226 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 227 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 228 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 229 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 230 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 231 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 234 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 235 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 236 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 237 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 238 because of missing atom number 6 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 240 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 241 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 242 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 243 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 244 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 245 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 248 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 249 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 250 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 251 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 252 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 253 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 254 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 255 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 256 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 257 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 258 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 260 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 261 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 262 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 263 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 264 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 265 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 266 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 267 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 268 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 269 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 270 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 273 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 274 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 275 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 276 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 277 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 278 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 279 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 282 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 283 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 284 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 285 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 287 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 289 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 291 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 292 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 293 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 294 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 295 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 296 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 297 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 298 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 299 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 300 because of missing atom number 5 atom name CB \ncore.pack.pack_rotamers: built 7982 rotamers at 274 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.docking.DockingProtocol: Score before repack:\nprotocols.docking.DockingProtocol: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.338 -1751.322 -591.947\n fa_rep 0.186 8417.226 1562.910\n fa_sol 0.242 975.051 235.962\n fa_elec 0.026 -338.684 -8.806\n fa_pair 0.164 -33.981 -5.573\n hbond_sr_bb 0.245 -47.347 -11.600\n hbond_lr_bb 0.245 -100.043 -24.511\n hbond_bb_sc 0.245 -24.902 -6.101\n hbond_sc 0.245 -6.857 -1.680\n dslf_ss_dst 0.500 -15.294 -7.647\n dslf_cs_ang 2.000 1.100 2.200\n dslf_ss_dih 5.000 0.462 2.308\n dslf_ca_dih 5.000 0.254 1.269\n fa_dun 0.036 1557.509 56.070\n---------------------------------------------------\n Total weighted score: 1202.856\ncore.pack.pack_rotamers: built 4094 rotamers at 291 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.docking.DockingProtocol: Score after repack:\nprotocols.docking.DockingProtocol: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.338 -1690.551 -571.406\n fa_rep 0.186 3035.584 563.647\n fa_sol 0.242 913.492 221.065\n fa_elec 0.026 -353.527 -9.192\n fa_pair 0.164 -37.809 -6.201\n hbond_sr_bb 0.245 -47.347 -11.600\n hbond_lr_bb 0.245 -100.043 -24.511\n hbond_bb_sc 0.245 -26.342 -6.454\n hbond_sc 0.245 -8.149 -1.996\n dslf_ss_dst 0.500 -15.294 -7.647\n dslf_cs_ang 2.000 1.100 2.200\n dslf_ss_dih 5.000 0.462 2.308\n dslf_ca_dih 5.000 0.254 1.269\n fa_dun 0.036 667.709 24.038\n---------------------------------------------------\n Total weighted score: 175.521\nprotocols.docking.DockMCMProtocol: in DockMCMProtocol.apply\nprotocols.docking.DockMCMProtocol: Using the DockingTaskFactory.\nprotocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockMCMCycle: /// Dockable Jumps: 1 ///\nprotocols.docking.DockMCMCycle: /// Translation: 0.1 ///\nprotocols.docking.DockMCMCycle: /// Rotation: 5 ///\nprotocols.docking.DockMCMCycle: /// Scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 0.338) (fa_rep 0.18568) (fa_sol 0.242) (fa_elec 0.026) (fa_pair 0.164) (hbond_sr_bb 0.245) (hbond_lr_bb 0.245) (hbond_bb_sc 0.245) (hbond_sc 0.245) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.036)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: /// Packing scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 0.338) (fa_rep 0.18568) (fa_sol 0.242) (fa_elec 0.026) (fa_pair 0.164) (hbond_sr_bb 0.245) (hbond_lr_bb 0.245) (hbond_bb_sc 0.245) (hbond_sc 0.245) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.036)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hb\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nWorking on decoy: dock_output_0.pdb\nonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1214 rotamers at 38 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 423 rotamers at 19 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 651 rotamers at 19 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 785 rotamers at 24 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 940 rotamers at 26 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 841 rotamers at 22 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.docking.DockingProtocol.metrics: unbound pose: \nprotocols.docking.DockingProtocol.metrics: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 1.000 -1625.788 -1625.788\n fa_rep 0.550 635.971 349.784\n fa_sol 1.000 858.723 858.723\n fa_intra_rep 0.005 774.341 3.872\n fa_intra_sol_xover4 1.000 50.611 50.611\n lk_ball_wtd 1.000 -37.926 -37.926\n fa_elec 1.000 -348.335 -348.335\n pro_close 1.250 102.522 128.153\n hbond_sr_bb 1.000 -47.347 -47.347\n hbond_lr_bb 1.000 -100.043 -100.043\n hbond_bb_sc 1.000 -36.544 -36.544\n hbond_sc 1.000 -10.049 -10.049\n dslf_fa13 1.250 -4.134 -5.168\n omega 0.400 32.147 12.859\n fa_dun 0.700 663.521 464.465\n p_aa_pp 0.600 -69.949 -41.970\n yhh_planarity 0.625 0.000 0.000\n ref 1.000 170.937 170.937\n rama_prepro 0.450 69.289 31.180\n---------------------------------------------------\n Total weighted score: -182.585\nprotocols.docking.DockingProtocol.metrics: bound pose: \nprotocols.docking.DockingProtocol.metrics: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 1.000 -1645.760 -1645.760\n fa_rep 0.550 640.173 352.095\n fa_sol 1.000 871.823 871.823\n fa_intra_rep 0.005 774.341 3.872\n fa_intra_sol_xover4 1.000 50.611 50.611\n lk_ball_wtd 1.000 -38.003 -38.003\n fa_elec 1.000 -348.063 -348.063\n pro_close 1.250 102.522 128.153\n hbond_sr_bb 1.000 -47.347 -47.347\n hbond_lr_bb 1.000 -100.043 -100.043\n hbond_bb_sc 1.000 -36.544 -36.544\n hbond_sc 1.000 -10.049 -10.049\n dslf_fa13 1.250 -4.134 -5.168\n omega 0.400 32.147 12.859\n fa_dun 0.700 663.521 464.465\n p_aa_pp 0.600 -69.949 -41.970\n yhh_planarity 0.625 0.000 0.000\n ref 1.000 170.937 170.937\n rama_prepro 0.450 69.289 31.180\n---------------------------------------------------\n Total weighted score: -186.952\nprotocols.docking.DockingProtocol.metrics: unbound energy: -182.585\nprotocols.docking.DockingProtocol.metrics: bound energy: -186.952\nprotocols.docking.DockingProtocol.metrics: interaction energy: -4.36676\nprotocols.docking.DockingProtocol.metrics: rb_jump: 1\nprotocols.docking.DockingProtocol.metrics: unbound pose: \nprotocols.docking.DockingProtocol.metrics: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.338 -1625.788 -549.516\n fa_rep 0.186 635.971 118.087\n fa_sol 0.242 858.723 207.811\n fa_elec 0.026 -348.335 -9.057\n fa_pair 0.164 -31.555 -5.175\n hbond_sr_bb 0.245 -47.347 -11.600\n hbond_lr_bb 0.245 -100.043 -24.511\n hbond_bb_sc 0.245 -25.378 -6.218\n hbond_sc 0.245 -8.347 -2.045\n dslf_ss_dst 0.500 -15.294 -7.647\n dslf_cs_ang 2.000 1.100 2.200\n dslf_ss_dih 5.000 0.462 2.308\n dslf_ca_dih 5.000 0.254 1.269\n fa_dun 0.036 663.521 23.887\n---------------------------------------------------\n Total weighted score: -260.206\nprotocols.docking.DockingProtocol.metrics: bound pose: \nprotocols.docking.DockingProtocol.metrics: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.338 -1645.760 -556.267\n fa_rep 0.186 640.173 118.867\n fa_sol 0.242 871.823 210.981\n fa_elec 0.026 -348.063 -9.050\n fa_pair 0.164 -33.488 -5.492\n hbond_sr_bb 0.245 -47.347 -11.600\n hbond_lr_bb 0.245 -100.043 -24.511\n hbond_bb_sc 0.245 -25.864 -6.337\n hbond_sc 0.245 -8.361 -2.048\n dslf_ss_dst 0.500 -15.294 -7.647\n dslf_cs_ang 2.000 1.100 2.200\n dslf_ss_dih 5.000 0.462 2.308\n dslf_ca_dih 5.000 0.254 1.269\n fa_dun 0.036 663.521 23.887\n---------------------------------------------------\n Total weighted score: -263.439\nprotocols.docking.DockingProtocol.metrics: unbound energy: -260.206\nprotocols.docking.DockingProtocol.metrics: bound energy: -263.439\nprotocols.docking.DockingProtocol.metrics: interaction energy: -3.23264\nprotocols.docking.DockingProtocol.metrics: rb_jump: 1\ncore.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/demo/D100_Docking.py:95: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.rigid import (\n\nFinished D100_Docking in 0:00:47.540108", "state": "passed"}, "D110_DNA_interface": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.10938 seconds.\ncore.import_pose.import_pose: File '../test/data/dna_test.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name O5* to O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name C5* to C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Number of nucleic acid residue fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: -12 C DG GUA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: P \ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C4'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 164 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 166 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 167 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 169 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 170 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 172 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 173 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 174 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:UpperRNA:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 175 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE:LowerDNA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 177 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 181 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 182 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 183 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 184 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 185 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 186 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT:UpperDNA\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for OP1 and OP2 for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 161\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N9 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N7 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C8 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: Connecting residues: 162 ( GUA:LowerDNA:VirtualDNAPhosphate ) and 163 ( CYT ) at atoms O3' and P \ncore.conformation.Conformation: with mutual distances: 0.293633 and 0.00610344\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 163 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 164 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 165 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 166 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 167 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 168 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 169 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 170 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 171 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 172 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 173 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 174 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 175 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 176 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 177 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 178 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 179 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 181 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 182 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 183 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 184 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 185 atom 2H2' (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 12 atom name N9 \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.25456 seconds to load from binary\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.docking.DockMCMProtocol: in DockMCMProtocol.apply\nprotocols.docking.DockMCMProtocol: Using the DockingTaskFactory.\nprotocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockMCMCycle: /// Dockable Jumps: 1 ///\nprotocols.docking.DockMCMCycle: /// Translation: 0.1 ///\nprotocols.docking.DockMCMCycle: /// Rotation: 5 ///\nprotocols.docking.DockMCMCycle: /// Scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 0.947733) (fa_rep 0.577238) (fa_sol 0.507356) (fa_elec 1) (pro_close 1) (hbond_sr_bb 2.80253) (hbond_lr_bb 2.80253) (hbond_bb_sc 2.80253) (hbond_sc 1.59624) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.68229) (p_aa_pp 0.612065) (ref 1) (res_type_constraint 1)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref -1.58548 -1.18225 3.39 1.61782 0.10405 -2.19778 0.838118 -1.81735 -1.53824 -1.26583 -1.40187 1.06144 -2.58097 -0.20752 9.93689 -2.59427 -1.18434 -1.42293 1.82099 0.209525\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: /// Packing scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \np\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nWorking on decoy: dna_output_0.pdb\nrotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 388 rotamers at 34 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \n\nFinished D110_DNA_interface in 0:00:41.036213", "state": "passed"}, "D120_Ligand_interface": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished D120_Ligand_interface in 0:00:16.238688", "state": "passed"}, "T000_Imports": {"log": "vector1_int[1, 2, 3, 4]\nvector1_double[1, 2, 3, 4.5]\nvector1_std_string[a, b, c, d]\nstd_set[1, 2, 3, 4]\nstd_set[1, 2, 3, 4.5]\nstd_set[a, b, c, d]\nTesting Python bindings for Rosetta...\nInit...\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ndevel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=861559990 seed_offset=0 real_seed=861559990\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=861559990 RG_type=mt19937\n\nFinished T000_Imports in 0:00:16.168424", "state": "passed"}, "T005_Bindings": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nTotal residues: 0\nSequence: \nFold tree:\nFOLD_TREE \nTotal residues: 0\nSequence: \nFold tree:\nFOLD_TREE \nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: false\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: false\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: false\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nrosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionOP() PASSED\nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: false\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: false\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: false\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nrosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP() PASSED\nScoreFunction::show():\nweights:\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: true\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: true\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: true\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nrosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP2() PASSED\n<pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x1031afc30>\n<pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x1031afc30>\n<pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x1031afc30>\n<pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x1031afc30>\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-492862494 seed_offset=0 real_seed=-492862494\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-492862494 RG_type=mt19937\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.974442 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T005_Bindings.py:48: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.toolbox.py_inheritance_test import *\n\nFinished T005_Bindings in 0:00:19.364618", "state": "passed"}, "T006_Options": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nout:nstruct: 5\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -nstruct 5 -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T006_Options in 0:00:16.009679", "state": "passed"}, "T007_TracerIO": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.02094 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n-------- Test/Demo for capturing Tracers output in PyRosetta --------\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\nCaptured IO:\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.02094 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nMyPyTracer.output_callback with argument:\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \n\nMyPyTracer.output_callback with argument:\n\nMyPyTracer.output_callback with argument:\ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\n\nMyPyTracer.output_callback with argument:\ncore.init: Rosetta extras: []\n\nMyPyTracer.output_callback with argument:\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\n\nMyPyTracer.output_callback with argument:\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1361329603 seed_offset=0 real_seed=1361329603\n\nMyPyTracer.output_callback with argument:\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1361329603 RG_type=mt19937\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1361329603 seed_offset=0 real_seed=1361329603\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1361329603 RG_type=mt19937\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T007_TracerIO.py:14: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n import rosetta, pyrosetta\n\nFinished T007_TracerIO in 0:00:17.263862", "state": "passed"}, "T008_Serialization": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=146439262 seed_offset=0 real_seed=146439262\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=146439262 RG_type=mt19937\n\nFinished T008_Serialization in 0:00:16.171045", "state": "passed"}, "T009_Exceptions": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nExceptions type: <class 'RuntimeError'>, message: \n\nFile: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/src/protocols/rosetta_scripts/RosettaScriptsParser.cc:514\nparser::protocol file must specify PROTOCOLS section\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1121791482 seed_offset=0 real_seed=-1121791482\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1121791482 RG_type=mt19937\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.03548 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n\nFinished T009_Exceptions in 0:00:20.208637", "state": "passed"}, "T010_LoadPDB": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.05101 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.285255 seconds to load from binary\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.022659 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.io.silent.SilentFileData: Reading all structures from ../test/data/test_in.silent\ncore.io.silent.SilentFileData: Finished reading 8 structures from ../test/data/test_in.silent\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n\nFinished T010_LoadPDB in 0:00:19.928631", "state": "passed"}, "T020_Pose_Bindings": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:26: DeprecationWarning: Pose.__len__ is deprecated, prefer 'pose.residues.__len__'.\n assert(len(pose1) == 8) # Deprecated\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:35: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for residue in pose1: # Deprecated\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:56: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'.\n assert(''.join([res.annotated_name() for res in pose1[1:9]]) == 'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]') # Deprecated\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T020_Pose_Bindings.py:57: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'.\n assert(''.join([res.annotated_name() for res in pose1[-6:8]]) == 'DEFGH') # Deprecated\n\nFinished T020_Pose_Bindings in 0:00:17.396050", "state": "passed"}, "T040_Types": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T040_Types in 0:00:16.168987", "state": "passed"}, "T100_basic": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nGeneral testing ----------------------------------------------\nCreating Pose object...\nPose from PDB...\nBuilding Pose from sequence...\nPDB file name: DSEEKFLR\nTotal residues: 21\nSequence: DSEEKFLRRIGRFGYGYGPYE\nFold tree:\nFOLD_TREE EDGE 1 21 -1 \nDump PDB...\naccessing pose attributes\nPDB file name: ../test/data/test_in.pdb\nTotal residues: 116\nSequence: DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL\nFold tree:\nFOLD_TREE EDGE 1 116 -1 \nthere are 116 residues in this pose object\nphi of residue 5 is -64.78549729348204\npsi of residue 5 is -39.712439411727274\nset phi of residue 5 to -60\nset psi of residue 5 to -50\naccessing residue 5 from pose\nResidue 5: ILE (ILE, I):\nBase: ILE\n Properties: POLYMER PROTEIN CANONICAL_AA HYDROPHOBIC ALIPHATIC BETA_BRANCHED_SIDECHAIN METALBINDING ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB CG1 CG2 CD1 HB 1HG1 2HG1 1HG2 2HG2 3HG2 1HD1 2HD1 3HD1\nAtom Coordinates:\n N : -2.53898, 36.4415, 79.2297\n CA : -1.97052, 36.1949, 80.5403\n C : -2.23109, 37.3858, 81.4325\n O : -2.50917, 37.2043, 82.6002\n CB : -0.453211, 35.963, 80.4929\n CG1: -0.175565, 34.5273, 80.077\n CG2: 0.172042, 36.261, 81.8574\n CD1: -0.927946, 33.5005, 80.9024\n H : -1.93862, 36.5194, 78.4212\n HA : -2.46732, 35.3543, 81.0219\n HB : -0.0182833, 36.6096, 79.7313\n 1HG1: -0.458733, 34.4327, 79.0287\n 2HG1: 0.8975, 34.3623, 80.1785\n 1HG2: 1.24765, 36.092, 81.8094\n 2HG2: -0.0204952, 37.2987, 82.1272\n 3HG2: -0.264762, 35.6037, 82.6097\n 1HD1: -0.681316, 32.4982, 80.5509\n 2HD1: -0.643714, 33.5961, 81.9508\n 3HD1: -2.00002, 33.6654, 80.801\nMirrored relative to coordinates in ResidueType: FALSE\n\naccessing atoms from residue 5\n-2.53898, 36.4415, 79.2297\nxyz of at5N: -2.53898489237762 36.44151978598334 79.22969355726434\nnorm of xyz at5N: <bound method PyCapsule.norm of <pyrosetta.rosetta.numeric.xyzVector_double_t object at 0x10deb2a70>>\nvector1_core_conformation_Atom[-2.53898, 36.4415, 79.2297, -1.97052, 36.1949, 80.5403, -2.23109, 37.3858, 81.4325, -2.50917, 37.2043, 82.6002, -0.453211, 35.963, 80.4929, -0.175565, 34.5273, 80.077, 0.172042, 36.261, 81.8574, -0.927946, 33.5005, 80.9024, -1.93862, 36.5194, 78.4212, -2.46732, 35.3543, 81.0219, -0.0182833, 36.6096, 79.7313, -0.458733, 34.4327, 79.0287, 0.8975, 34.3623, 80.1785, 1.24765, 36.092, 81.8094, -0.0204952, 37.2987, 82.1272, -0.264762, 35.6037, 82.6097, -0.681316, 32.4982, 80.5509, -0.643714, 33.5961, 81.9508, -2.00002, 33.6654, 80.801]\nbond length of N-CA in residue 5 is \n1.4496692726273892\nbond angle of N-CA-C in residue 5 is \n1.9094258533068345\nsetting bond length of N-CA in residue 5 to 1.5A \nsetting bond angle of N-CA-C in residue 5 to 90 \npose was generated from this pdb file: ../test/data/test_in.pdb\npose numbering for chain A, residue 5, is 5\npdb chain letter and residue number for residue 5, is 5 A \nResidue 0: ALA (ALA, A):\nBase: ALA\n Properties: POLYMER PROTEIN CANONICAL_AA ALIPHATIC METALBINDING ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB 1HB 2HB 3HB \nAtom Coordinates:\n N : 0, 0, 0\n CA : 1.458, 0, 0\n C : 2.00885, 1.42017, 0\n O : 1.38304, 2.33899, -0.528697\n CB : 1.9878, -0.772763, -1.19909\n H : -0.491969, 0.763905, -0.44104\n HA : 1.79666, -0.489627, 0.91315\n 1HB : 3.07772, -0.76375, -1.18511\n 2HB : 1.63286, -1.80244, -1.15412\n 3HB : 1.63327, -0.30698, -2.11716\nMirrored relative to coordinates in ResidueType: FALSE\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.99567 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.022327 seconds.\n\nFinished T100_basic in 0:00:17.367896", "state": "passed"}, "T110_numeric": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T110_numeric in 0:00:16.167955", "state": "passed"}, "T120_core.RotamerSets": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-12516515 seed_offset=0 real_seed=-12516515\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-12516515 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.14304 seconds.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\n\nFinished T120_core.RotamerSets in 0:00:05.385981", "state": "passed"}, "T121_core.ResidueSelector": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nF.\n======================================================================\nFAIL: test_residue_selector_ctors (__main__.TestResidueSelectors)\n----------------------------------------------------------------------\nTraceback (most recent call last):\n File \"/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T121_core.ResidueSelector.py\", line 143, in test_residue_selector_ctors\n self.assertListEqual(selector_1.get_residues(pose), selector_2.get_residues(pose))\nAssertionError: Lists differ: [1, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] != [2, 4, 6]\n\nFirst differing element 0:\n1\n2\n\nFirst list contains 11 additional elements.\nFirst extra element 3:\n7\n\n- [1, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17]\n+ [2, 4, 6]\n\n----------------------------------------------------------------------\nRan 2 tests in 10.199s\n\nFAILED (failures=1)\n\nFinished T121_core.ResidueSelector in 0:00:12.822412", "state": "failed"}, "T150_PyMOL_Integration": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.12589 seconds.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.256127 seconds to load from binary\n\nFinished T150_PyMOL_Integration in 0:00:06.129454", "state": "passed"}, "T150_core.misc.lkball": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n1 1\n2 0\n3 0\n4 2\n5 0\n6 0\n7 2\n8 2\n9 0\n10 0\n11 0\n12 0\n13 0\n14 0\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1294291378 seed_offset=0 real_seed=-1294291378\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1294291378 RG_type=mt19937\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.10469 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.249673 seconds to load from binary\n\nFinished T150_core.misc.lkball in 0:00:06.093700", "state": "passed"}, "T190_Bindings_Utility": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T190_Bindings_Utility in 0:00:02.447673", "state": "passed"}, "T200_Scoring": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nScoring ----------------------------------------------\nCreating standard fullatom score function and scoring\nCreating standard centroid score function and scoring\nCreating standard score function and scoring, again\nCreating standard score from scratch\nAdjusting weights and scoring\nweight for fa_atr set to: 1.0\nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 1) (fa_pair 1)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: true\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: true\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: true\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nScore break down for pose...\nall residue energies are\nNone\nweighted energies for residue 5\nNone\n fa_atr: -0.593 fa_rep: 0.118 fa_pair: 0.000\nfa_atr of residue 5\n-0.5929040959214456\nfa_atr for residue 5: -0.5929040959214456\nmanually calculating 2body context-independent energies between residues 4 and 5\nfa_atr between 1 and 2: -0.42118788604496193\nfa_pair between 1 and 2: 0.0\nfa_rep between 1 and 2: 0.12092691972750393\nScoreType.fa_atrScoreType.fa_repScoreType.fa_solScoreType.fa_intra_atrScoreType.fa_intra_repScoreType.fa_intra_solScoreType.fa_intra_atr_xover4ScoreType.fa_intra_rep_xover4ScoreType.fa_intra_sol_xover4ScoreType.fa_intra_atr_nonproteinScoreType.fa_intra_rep_nonproteinScoreType.fa_intra_sol_nonproteinScoreType.fa_intra_RNA_base_phos_atrScoreType.fa_intra_RNA_base_phos_repScoreType.fa_intra_RNA_base_phos_solScoreType.fa_atr_dummyScoreType.fa_rep_dummyScoreType.fa_sol_dummyScoreType.fa_vdw_tinkerScoreType.lk_hackScoreType.lk_ballScoreType.lk_ball_wtdScoreType.lk_ball_isoScoreType.lk_ball_bridgeScoreType.lk_ball_bridge_uncplScoreType.lk_domeScoreType.lk_dome_isoScoreType.lk_dome_bridgeScoreType.lk_dome_bridge_uncplScoreType.lk_ball_bridge2ScoreType.lk_ball_bridge_uncpl2ScoreType.lk_dome_packScoreType.coarse_fa_atrScoreType.coarse_fa_repScoreType.coarse_fa_solScoreType.coarse_beadljScoreType.mm_lj_intra_repScoreType.mm_lj_intra_atrScoreType.mm_lj_inter_repScoreType.mm_lj_inter_atrScoreType.mm_twistScoreType.mm_bendScoreType.mm_stretchScoreType.lk_costhetaScoreType.lk_polarScoreType.lk_nonpolarScoreType.lk_polar_intra_RNAScoreType.lk_nonpolar_intra_RNAScoreType.fa_elecScoreType.fa_elec_bb_bbScoreType.fa_elec_bb_scScoreType.fa_elec_sc_scScoreType.fa_intra_elecScoreType.fa_imm_elecScoreType.h2o_hbondScoreType.dna_drScoreType.dna_bpScoreType.dna_bsScoreType.dna_refScoreType.peptide_bondScoreType.pcsScoreType.pcsTs1ScoreType.pcsTs2ScoreType.pcsTs3ScoreType.pcsTs4ScoreType.pcs2ScoreType.fastsaxsScoreType.saxs_scoreScoreType.saxs_cen_scoreScoreType.saxs_fa_scoreScoreType.pddf_scoreScoreType.fiberdiffractionScoreType.fiberdiffractiondensScoreType.epr_deer_scoreScoreType.fa_mbenvScoreType.fa_mbsolvScoreType.fa_elec_rna_phos_phosScoreType.fa_elec_rna_phos_sugrScoreType.fa_elec_rna_phos_baseScoreType.fa_elec_rna_sugr_sugrScoreType.fa_elec_rna_sugr_baseScoreType.fa_elec_rna_base_baseScoreType.fa_elec_rna_phos_phos_fastScoreType.fa_elec_rna_phos_sugr_fastScoreType.fa_elec_rna_phos_base_fastScoreType.fa_elec_rna_sugr_sugr_fastScoreType.fa_elec_rna_sugr_base_fastScoreType.fa_elec_rna_base_base_fastScoreType.fa_elec_aro_aroScoreType.fa_elec_aro_allScoreType.hack_aroScoreType.rna_fa_atr_baseScoreType.rna_fa_rep_baseScoreType.rna_data_backboneScoreType.ch_bondScoreType.ch_bond_bb_bbScoreType.ch_bond_sc_scScoreType.ch_bond_bb_scScoreType.pro_closeScoreType.rama2bScoreType.vdwScoreType.cenpackScoreType.cenpack_smoothScoreType.cen_hbScoreType.hybrid_vdwScoreType.gaussScoreType.rna_vdwScoreType.rnp_vdwScoreType.rna_base_backboneScoreType.rna_backbone_backboneScoreType.rna_repulsiveScoreType.rna_base_pair_pairwiseScoreType.rna_base_axis_pairwiseScoreType.rna_base_stagger_pairwiseScoreType.rna_base_stack_pairwiseScoreType.rna_base_stack_axis_pairwiseScoreType.rna_data_baseScoreType.rna_base_pairScoreType.rna_base_axisScoreType.rna_base_staggerScoreType.rna_base_stackScoreType.rna_base_stack_axisScoreType.rnp_base_pairScoreType.rnp_stackScoreType.rnp_stack_xyScoreType.rnp_pairScoreType.rnp_pair_distScoreType.rnp_aa_to_rna_backboneScoreType.rna_mg_pointScoreType.rna_mg_point_indirectScoreType.mgScoreType.mg_ligScoreType.mg_solScoreType.mg_refScoreType.hoh_refScoreType.rna_torsionScoreType.rna_torsion_scScoreType.rna_suiteScoreType.rna_jr_suiteScoreType.suiteness_bonusScoreType.tna_suiteScoreType.rna_sugar_closeScoreType.fa_stackScoreType.fa_stack_lowerScoreType.fa_stack_upperScoreType.fa_stack_aroScoreType.fa_stack_extScoreType.fa_stack_solScoreType.fa_stack_lrScoreType.fa_stack_rna_proteinScoreType.fa_stack_rna_protein_aroScoreType.ss_contact_worstScoreType.stack_elecScoreType.stack_elec_base_baseScoreType.stack_elec_base_bbScoreType.alignmentScoreType.dna_bb_torsionScoreType.dna_sugar_closeScoreType.dna_base_distanceScoreType.geom_sol_fastScoreType.geom_sol_fast_intra_RNAScoreType.fa_cust_pair_distScoreType.custom_atom_pairScoreType.orbitals_hpol_bbScoreType.pci_cation_piScoreType.pci_pi_piScoreType.pci_salt_bridgeScoreType.pci_hbondScoreType.arg_cation_piScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_lastScoreType.pythonScoreType.fa_pairScoreType.fa_pair_aro_aroScoreType.fa_pair_aro_polScoreType.fa_pair_pol_polScoreType.hbond_sr_bbScoreType.hbond_lr_bbScoreType.hbond_bb_scScoreType.hbond_sr_bb_scScoreType.hbond_lr_bb_scScoreType.hbond_scScoreType.hbond_intraScoreType.hbond_watScoreType.wat_entropyScoreType.hbondScoreType.npd_hbond_sr_bbScoreType.npd_hbond_lr_bbScoreType.npd_hbond_bb_scScoreType.npd_hbond_sr_bb_scScoreType.npd_hbond_lr_bb_scScoreType.npd_hbond_scScoreType.npd_hbond_intraScoreType.npd_hbondScoreType.fa_grpelecScoreType.PyRosettaTwoBodyContextDependentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextDependentEnergy_lastScoreType.interface_dd_pairScoreType.geom_solScoreType.geom_sol_intra_RNAScoreType.occ_sol_fittedScoreType.occ_sol_fitted_onebodyScoreType.occ_sol_exactScoreType.cen_rot_pairScoreType.cen_rot_pair_angScoreType.cen_rot_pair_dihScoreType.pairScoreType.cen_pair_smoothScoreType.MpairScoreType.MPPairScoreType.FaMPSolvScoreType.suckScoreType.rna_rgScoreType.rna_motifScoreType.facts_elecScoreType.facts_solvScoreType.facts_sasaScoreType.motif_dockScoreType.pointwaterScoreType.goapScoreType.goap_distScoreType.goap_angleScoreType.approximate_buried_unsat_penaltyScoreType.interchain_pairScoreType.interchain_vdwScoreType.gb_elecScoreType.multipole_elecScoreType.fa_sasaScoreType.dslf_ss_dstScoreType.dslf_cs_angScoreType.dslf_ss_dihScoreType.dslf_ca_dihScoreType.dslf_cbs_dsScoreType.dslf_fa13ScoreType.dslfc_cen_dstScoreType.dslfc_cb_dstScoreType.dslfc_angScoreType.dslfc_cb_dihScoreType.dslfc_bb_dihScoreType.dslfc_rotScoreType.dslfc_transScoreType.dslfc_RTScoreType.atom_pair_constraintScoreType.base_pair_constraintScoreType.coarse_chainbreak_constraintScoreType.constant_constraintScoreType.coordinate_constraintScoreType.angle_constraintScoreType.dihedral_constraintScoreType.big_bin_constraintScoreType.dunbrack_constraintScoreType.site_constraintScoreType.metalhash_constraintScoreType.metalbinding_constraintScoreType.rna_stub_coord_hackScoreType.bond_geometryScoreType.rna_bond_geometryScoreType.Hpol_bond_geometryScoreType.ramaScoreType.omegaScoreType.fa_dunScoreType.fa_dun_devScoreType.fa_dun_rotScoreType.fa_dun_semiScoreType.cen_rot_dunScoreType.dna_chiScoreType.p_aa_ppScoreType.p_aa_ssScoreType.yhh_planarityScoreType.hxl_torsScoreType.h2o_intraScoreType.refScoreType.ref_ncScoreType.seqdep_refScoreType.nmer_refScoreType.nmer_pssmScoreType.nmer_svmScoreType.envsmoothScoreType.e_pHScoreType.rna_bulgeScoreType.dna_dihedral_bbScoreType.dna_dihedral_chiScoreType.dna_dihedral_sugarScoreType.sugar_bbScoreType.free_suiteScoreType.free_2HOprimeScoreType.free_side_chainScoreType.free_baseScoreType.free_resScoreType.free_dofScoreType.intermolScoreType.other_poseScoreType.special_rotScoreType.PB_elecScoreType.cen_env_smoothScoreType.cbeta_smoothScoreType.cen_rot_envScoreType.cen_rot_cbetaScoreType.envScoreType.cbetaScoreType.DFIREScoreType.MenvScoreType.McbetaScoreType.Menv_non_helixScoreType.Menv_terminiScoreType.Menv_tm_projScoreType.MlipoScoreType.rgScoreType.rg_localScoreType.coScoreType.hs_pairScoreType.ss_pairScoreType.rsigmaScoreType.sheetScoreType.burial_v2ScoreType.burialScoreType.abegoScoreType.covalent_labelingScoreType.covalent_labeling_faScoreType.hrf_ms_labelingScoreType.hrf_dynamicsScoreType.ccs_immsScoreType.depc_msScoreType.rnp_envScoreType.loop_closeScoreType.missing_resScoreType.MPEnvScoreType.MPCbetaScoreType.MPLipoScoreType.MPTerminiScoreType.MPNonHelixScoreType.MPTMProjScoreType.FaMPEnvScoreType.FaMPEnvSmoothScoreType.fa_water_to_bilayerScoreType.f_elec_lipidlayerScoreType.FaMPAsymEzCBScoreType.FaMPAsymEzCGScoreType.MPResidueLipophilicityScoreType.span_insScoreType.mp_span_angScoreType.MPHelicalityScoreType.natbias_ssScoreType.natbias_hsScoreType.natbias_hhScoreType.natbias_stwistScoreType.aa_cmpScoreType.dock_ens_confScoreType.csaScoreType.dcScoreType.rdcScoreType.rdc_segmentsScoreType.rdc_rohlScoreType.nmr_pcsScoreType.nmr_rdcScoreType.nmr_preScoreType.cen_pair_motifsScoreType.cen_pair_motif_degreeScoreType.holesScoreType.holes_decoyScoreType.holes_reslScoreType.holes_minScoreType.holes_min_meanScoreType.rna_chem_shiftScoreType.rna_chem_mapScoreType.rna_chem_map_loresScoreType.rna_partitionScoreType.dab_sasaScoreType.dab_sevScoreType.saScoreType.d2h_saScoreType.ProQMScoreType.ProQScoreType.interchain_envScoreType.interchain_contactScoreType.chainbreakScoreType.linear_chainbreakScoreType.overlap_chainbreakScoreType.distance_chainbreakScoreType.dof_constraintScoreType.branch_connScoreType.linear_branch_connScoreType.rama_preproScoreType.paa_abego3ScoreType.cart_bondedScoreType.cart_bonded_angleScoreType.cart_bonded_lengthScoreType.cart_bonded_ringScoreType.cart_bonded_torsionScoreType.cart_bonded_properScoreType.cart_bonded_improperScoreType.gen_bondedScoreType.gen_bonded_bondScoreType.gen_bonded_angleScoreType.gen_bonded_torsionScoreType.gen_bonded_improperScoreType.neigh_vectScoreType.neigh_countScoreType.neigh_vect_rawScoreType.symE_bonusScoreType.sym_ligScoreType.mhc_epitopeScoreType.pack_statScoreType.rmsScoreType.res_type_constraintScoreType.res_type_linking_constraintScoreType.pocket_constraintScoreType.backbone_stub_constraintScoreType.backbone_stub_linear_constraintScoreType.surfaceScoreType.p_aaScoreType.unfoldedScoreType.split_unfolded_two_bodyScoreType.fa_atr_refScoreType.fa_rep_refScoreType.fa_sol_refScoreType.fa_elec_refScoreType.hbond_refScoreType.dslf_fa13_refScoreType.fa_intra_atr_refScoreType.fa_intra_rep_refScoreType.fa_intra_sol_refScoreType.pro_close_refScoreType.fa_dun_refScoreType.fa_dun_dev_refScoreType.fa_dun_rot_refScoreType.fa_dun_semi_refScoreType.rama_refScoreType.p_aa_pp_refScoreType.omega_refScoreType.mm_lj_intra_rep_refScoreType.mm_lj_intra_atr_refScoreType.mm_twist_refScoreType.elec_dens_fastScoreType.elec_dens_windowScoreType.elec_dens_whole_structure_caScoreType.elec_dens_whole_structure_allatomScoreType.elec_dens_atomwiseScoreType.grid_vdwScoreType.xtal_mlScoreType.xtal_rworkScoreType.xtal_rfreeScoreType.hpatchScoreType.Menv_smoothScoreType.wat_desolvScoreType.ring_closeScoreType.aa_repeatScoreType.aa_compositionScoreType.aspartimide_penaltyScoreType.hbnetScoreType.buried_unsatisfied_penaltyScoreType.netchargeScoreType.voids_penaltyScoreType.sap_constraintScoreType.dna_envScoreType.dna_pairScoreType.dump_trajectoryScoreType.PyRosettaEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaEnergy_lastScoreType.sidechain_neighborsScoreType.target_clashScoreType.membrane_span_constraintScoreType.membrane_span_term_z_constraintScoreType.aromatic_restraintScoreType.rna_coarse_distScoreType.total_scoreScoreType.dummy_score_type\nidentifying hydrogen bonds in structure\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.11472 seconds.\ncore.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.248058 seconds to load from binary\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 1.000 -5.202 -5.202\n fa_rep 1.000 1.049 1.049\n fa_pair 1.000 0.000 0.000\n---------------------------------------------------\n Total weighted score: -4.153\ncore.scoring.Energies: E fa_atr fa_rep fa_pair\ncore.scoring.Energies: E(i) 1 -0.30 0.06 0.00\ncore.scoring.Energies: E(i) 2 -0.51 0.12 0.00\ncore.scoring.Energies: E(i) 3 -0.60 0.11 0.00\ncore.scoring.Energies: E(i) 4 -0.59 0.12 0.00\ncore.scoring.Energies: E(i) 5 -0.59 0.12 0.00\ncore.scoring.Energies: E(i) 6 -0.60 0.11 0.00\ncore.scoring.Energies: E(i) 7 -0.60 0.11 0.00\ncore.scoring.Energies: E(i) 8 -0.59 0.12 0.00\ncore.scoring.Energies: E(i) 9 -0.52 0.12 0.00\ncore.scoring.Energies: E(i) 10 -0.31 0.06 0.00\ncore.scoring.Energies: total_energy fa_atr -5.202\ncore.scoring.Energies: total_energy fa_rep 1.049\ncore.scoring.Energies: total_energy fa_pair 0.000\ncore.scoring.Energies: E fa_atr fa_rep fa_pair\ncore.scoring.Energies: E(i) 5 -0.59 0.12 0.00\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\ncore.scoring.hbonds.HBondSet: #A 6 HIS N A 2 ALA O 2.04 144.3 129.5 -90.7 1.000 -0.591\ncore.scoring.hbonds.HBondSet: #A 8 ILE N A 4 THR O 2.02 165.0 165.8 -132.1 1.000 -1.102\ncore.scoring.hbonds.HBondSet: #A 9 LEU N A 5 ILE O 2.26 163.0 149.7 -108.0 1.000 -0.865\ncore.scoring.hbonds.HBondSet: #A 10 ASP N A 7 SER O 1.99 118.8 121.9 -72.7 1.000 -0.053\ncore.scoring.hbonds.HBondSet: #A 11 TRP N A 7 SER O 2.13 163.6 152.7 150.3 1.000 -1.338\ncore.scoring.hbonds.HBondSet: #A 12 ILE N A 8 ILE O 2.03 139.2 140.6 -123.7 1.000 -0.721\ncore.scoring.hbonds.HBondSet: #A 13 GLU N A 9 LEU O 2.04 165.1 162.3 -156.5 1.000 -1.224\ncore.scoring.hbonds.HBondSet: #A 14 ASP N A 10 ASP O 1.86 150.2 152.5 -107.8 1.000 -0.689\ncore.scoring.hbonds.HBondSet: #A 15 ASN ND2A 11 TRP O 1.74 167.5 145.0 55.4 0.576 -1.075\ncore.scoring.hbonds.HBondSet: #A 15 ASN N A 12 ILE O 1.90 129.6 117.0 -123.3 1.000 -0.502\ncore.scoring.hbonds.HBondSet: #A 16 LEU N A 12 ILE O 2.12 139.7 156.3 41.7 1.000 -0.648\ncore.scoring.hbonds.HBondSet: #A 51 TYR OH A 13 GLU OE1 2.33 127.5 132.6 175.2 0.694 -0.057\ncore.scoring.hbonds.HBondSet: #A 55 ARG NH1A 13 GLU OE2 1.34 170.5 131.0 -58.3 0.812 -0.243\ncore.scoring.hbonds.HBondSet: #A 18 SER N A 15 ASN O 2.25 125.4 126.6 135.8 1.000 -0.507\ncore.scoring.hbonds.HBondSet: #A 56 LYS NZ A 19 PRO O 2.09 136.2 127.1 -155.2 0.835 -0.338\ncore.scoring.hbonds.HBondSet: #A 26 SER N A 22 LEU O 1.89 153.1 161.7 -159.5 1.000 -0.965\ncore.scoring.hbonds.HBondSet: #A 27 GLU N A 23 GLU O 1.90 127.2 124.4 -127.4 1.000 -0.529\ncore.scoring.hbonds.HBondSet: #A 28 ARG N A 24 LYS O 2.13 151.6 161.0 139.1 1.000 -0.876\ncore.scoring.hbonds.HBondSet: #A 30 GLY N A 28 ARG O 2.49 110.6 116.7 -151.7 1.000 -0.033\ncore.scoring.hbonds.HBondSet: #A 35 HIS N A 32 SER OG 2.29 149.9 129.3 42.4 0.412 -1.133\ncore.scoring.hbonds.HBondSet: #A 36 LEU N A 32 SER O 2.00 150.7 167.4 51.1 1.000 -0.802\ncore.scoring.hbonds.HBondSet: #A 37 GLN N A 33 LYS O 2.10 152.4 144.0 -111.3 1.000 -0.862\ncore.scoring.hbonds.HBondSet: #A 38 ARG N A 34 TRP O 2.05 155.6 134.2 -129.9 1.000 -1.268\ncore.scoring.hbonds.HBondSet: #A 39 MET N A 35 HIS O 1.83 162.3 167.2 121.8 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #A 40 PHE N A 36 LEU O 2.00 162.8 150.8 -90.5 1.000 -1.000\ncore.scoring.hbonds.HBondSet: #A 41 LYS N A 37 GLN O 1.92 156.7 151.5 -106.1 1.000 -0.897\ncore.scoring.hbonds.HBondSet: #A 42 LYS N A 38 ARG O 2.04 174.7 160.8 -124.7 1.000 -1.211\ncore.scoring.hbonds.HBondSet: #A 43 GLU N A 39 MET O 1.81 133.8 142.7 -148.9 1.000 -0.720\ncore.scoring.hbonds.HBondSet: #A 44 THR N A 40 PHE O 1.84 148.2 139.0 -104.0 1.000 -0.626\ncore.scoring.hbonds.HBondSet: #A 46 HIS N A 44 THR OG1 2.38 140.9 115.1 31.0 0.647 -0.563\ncore.scoring.hbonds.HBondSet: #A 51 TYR N A 47 SER O 2.31 143.2 157.6 -134.7 1.000 -0.475\ncore.scoring.hbonds.HBondSet: #A 52 ILE N A 48 LEU O 2.04 169.5 172.7 -140.4 1.000 -1.110\ncore.scoring.hbonds.HBondSet: #A 53 ARG N A 49 GLY O 2.27 160.5 141.5 -138.6 1.000 -1.219\ncore.scoring.hbonds.HBondSet: #A 54 SER N A 50 GLN O 2.03 139.9 119.8 -107.0 1.000 -0.580\ncore.scoring.hbonds.HBondSet: #A 55 ARG N A 51 TYR O 1.91 145.7 149.7 -119.9 1.000 -0.733\ncore.scoring.hbonds.HBondSet: #A 56 LYS N A 52 ILE O 2.05 152.8 145.5 -144.7 1.000 -1.268\ncore.scoring.hbonds.HBondSet: #A 57 MET N A 53 ARG O 1.90 161.7 154.0 -106.5 1.000 -0.970\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 54 SER O 2.05 153.5 133.7 -110.9 1.000 -0.941\ncore.scoring.hbonds.HBondSet: #A 59 GLU N A 55 ARG O 2.06 152.9 137.4 -113.4 1.000 -0.939\ncore.scoring.hbonds.HBondSet: #A 55 ARG NE A 113 LEU O 2.13 147.9 119.9 -95.9 0.859 -0.450\ncore.scoring.hbonds.HBondSet: #A 55 ARG NH2A 113 LEU O 1.82 143.4 172.4 178.3 0.859 -0.454\ncore.scoring.hbonds.HBondSet: #A 60 ILE N A 56 LYS O 1.92 158.0 145.1 -109.1 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 56 LYS NZ A 78 TYR O 1.99 147.6 161.9 -149.3 0.976 -0.347\ncore.scoring.hbonds.HBondSet: #A 61 ALA N A 57 MET O 2.19 141.3 144.0 -107.9 1.000 -0.481\ncore.scoring.hbonds.HBondSet: #A 62 GLN N A 58 THR O 2.32 147.4 145.9 -134.5 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #A 63 LYS N A 59 GLU O 2.38 148.8 139.1 -123.6 1.000 -0.599\ncore.scoring.hbonds.HBondSet: #A 78 TYR OH A 59 GLU OE1 2.33 163.0 127.0 55.3 0.882 -0.201\ncore.scoring.hbonds.HBondSet: #A 64 LEU N A 60 ILE O 2.21 144.1 134.6 -117.2 1.000 -0.669\ncore.scoring.hbonds.HBondSet: #A 66 GLU N A 62 GLN O 2.15 126.2 128.1 -135.5 1.000 -0.625\ncore.scoring.hbonds.HBondSet: #A 102 ARG NH1A 64 LEU O 2.20 150.3 103.2 -43.0 0.859 -0.641\ncore.scoring.hbonds.HBondSet: #A 69 GLU N A 67 SER OG 1.98 163.8 131.5 73.0 0.459 -2.039\ncore.scoring.hbonds.HBondSet: #A 77 ARG NH2A 69 GLU OE1 2.08 111.0 127.8 164.8 0.600 -0.556\ncore.scoring.hbonds.HBondSet: #A 102 ARG NH2A 69 GLU O 1.73 172.3 129.2 104.5 0.647 -0.841\ncore.scoring.hbonds.HBondSet: #A 74 LEU N A 70 PRO O 2.10 138.8 143.2 -162.9 1.000 -1.132\ncore.scoring.hbonds.HBondSet: #A 75 ALA N A 71 ILE O 1.85 153.0 140.3 -108.4 1.000 -0.788\ncore.scoring.hbonds.HBondSet: #A 76 GLU N A 72 LEU O 2.12 179.0 157.2 -97.9 1.000 -1.108\ncore.scoring.hbonds.HBondSet: #A 77 ARG N A 73 TYR O 2.25 145.4 127.3 -111.3 1.000 -0.591\ncore.scoring.hbonds.HBondSet: #A 78 TYR N A 74 LEU O 2.27 139.7 142.0 -109.7 1.000 -0.357\ncore.scoring.hbonds.HBondSet: #A 80 PHE N A 75 ALA O 1.93 151.5 158.1 109.3 1.000 -0.785\ncore.scoring.hbonds.HBondSet: #A 85 THR N A 82 SER OG 2.28 168.9 144.9 9.5 0.482 -0.986\ncore.scoring.hbonds.HBondSet: #A 86 LEU N A 82 SER O 2.39 154.0 131.8 -121.2 1.000 -0.707\ncore.scoring.hbonds.HBondSet: #A 87 THR N A 83 GLN O 1.58 162.4 157.0 -131.4 1.000 -0.163\ncore.scoring.hbonds.HBondSet: #A 88 ARG N A 84 GLN O 1.93 164.6 148.5 -104.7 1.000 -1.041\ncore.scoring.hbonds.HBondSet: #A 89 THR N A 85 THR O 2.15 160.7 139.8 -119.7 1.000 -1.116\ncore.scoring.hbonds.HBondSet: #A 90 PHE N A 86 LEU O 1.84 164.3 149.9 -87.9 1.000 -0.895\ncore.scoring.hbonds.HBondSet: #A 91 LYS N A 87 THR O 2.05 156.2 143.4 -111.4 1.000 -0.976\ncore.scoring.hbonds.HBondSet: #A 92 ASN N A 88 ARG O 2.11 145.3 137.3 -113.7 1.000 -0.732\ncore.scoring.hbonds.HBondSet: #A 93 TYR N A 89 THR O 2.20 132.5 141.4 -131.1 1.000 -0.528\ncore.scoring.hbonds.HBondSet: #A 93 TYR N A 90 PHE O 2.17 133.3 101.2 -94.2 1.000 -0.015\ncore.scoring.hbonds.HBondSet: #A 94 PHE N A 90 PHE O 1.91 148.0 158.2 -147.9 1.000 -0.887\ncore.scoring.hbonds.HBondSet: #A 95 ASP N A 91 LYS O 1.86 129.3 118.4 -77.4 1.000 -0.164\ncore.scoring.hbonds.HBondSet: #A 93 TYR OH A 111 ARG O 1.83 153.2 166.2 98.5 0.624 -0.510\ncore.scoring.hbonds.HBondSet: #A 111 ARG NH1A 93 TYR O 2.39 132.6 132.2 -117.9 0.624 -0.001\ncore.scoring.hbonds.HBondSet: #A 111 ARG NH1A 95 ASP OD2 1.88 140.2 140.4 -85.8 0.435 -0.369\ncore.scoring.hbonds.HBondSet: #A 111 ARG NH2A 95 ASP OD2 1.97 137.7 130.0 27.8 0.435 -1.037\ncore.scoring.hbonds.HBondSet: #A 101 TYR N A 97 PRO O 2.06 151.2 145.9 -135.7 1.000 -1.111\ncore.scoring.hbonds.HBondSet: #A 102 ARG N A 98 PRO O 2.03 134.2 138.7 -133.9 1.000 -0.762\ncore.scoring.hbonds.HBondSet: #A 103 MET N A 99 HIS O 2.13 143.0 152.2 -153.1 1.000 -0.914\ncore.scoring.hbonds.HBondSet: #A 112 PHE N A 109 GLU O 2.04 153.8 151.0 -144.0 1.000 -1.177\ncore.scoring.hbonds.HBondSet: #A 114 HIS NE2A 109 GLU OE2 2.35 163.9 126.7 64.4 0.388 -0.463\ncore.scoring.hbonds.HBondSet: #A 116 LEU N A 114 HIS O 1.65 145.1 121.9 -164.6 1.000 -1.004\n\nFinished T200_Scoring in 0:00:06.666680", "state": "passed"}, "T201_Scoring_pre_talaris": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -restore_pre_talaris_2013_behavior -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-40681057 seed_offset=0 real_seed=-40681057\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-40681057 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 74 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.058638 seconds.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp\nbasic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack library took 0.067042 seconds to load from binary\n\nFinished T201_Scoring_pre_talaris in 0:00:05.172056", "state": "passed"}, "T220_AtomAtomPairEnergies": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.98315 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] miss\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n\n\n\nPrinting individual energies:\nres-res atr score emap: -2.5584311767440906\nres-res atr score pairwise: -2.5584311767440906\nres-res rep score emap: 3.515015877828057\nres-res rep score pairwise: 3.515015877828057\nres-res solv score emap: 0.7697815585356838\nres-res solv score pairwise: 0.7697815585356838\nChecking if scores match...\nScore did match, yay...\ning heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.240181 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished T220_AtomAtomPairEnergies in 0:00:06.750641", "state": "passed"}, "T250_Constraints": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nconstraints ----------------------------------------------\n\nScore before constraints applied: 949.3120641217009\nScore after constraints applied: 1195.8122748998228\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.14181 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.234482 seconds to load from binary\n\nFinished T250_Constraints in 0:00:06.289378", "state": "passed"}, "T300_PyJobDistributor": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nWorking on decoy: _jd_test_4.pdb\nWorking on decoy: _jd_test_3.pdb\nWorking on decoy: _jd_test_9.pdb\nWorking on decoy: _jd_test_8.pdb\nWorking on decoy: _jd_test_7.pdb\nWorking on decoy: _jd_test_0.pdb\nWorking on decoy: _jd_test_1.pdb\nWorking on decoy: _jd_test_2.pdb\nWorking on decoy: _jd_test_5.pdb\nWorking on decoy: _jd_test_6.pdb\nWorking on decoy: _jd_at_test_7.pdb.gz\nWorking on decoy: _jd_at_test_1.pdb.gz\nWorking on decoy: _jd_at_test_0.pdb.gz\nWorking on decoy: _jd_at_test_2.pdb.gz\nWorking on decoy: _jd_at_test_4.pdb.gz\nWorking on decoy: _jd_at_test_8.pdb.gz\nWorking on decoy: _jd_at_test_3.pdb.gz\nWorking on decoy: _jd_at_test_9.pdb.gz\nWorking on decoy: _jd_at_test_5.pdb.gz\nWorking on decoy: _jd_at_test_6.pdb.gz\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.04654 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.239365 seconds to load from binary\n\nFinished T300_PyJobDistributor in 0:00:06.373430", "state": "passed"}, "T400_Refinement": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.980809 seconds.\ncore.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10\ncore.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10\n resnum BB CHI NU BRANCH\n 001 TRUE FALSE FALSE FALSE\n 002 TRUE FALSE FALSE FALSE\n 003 TRUE FALSE FALSE FALSE\n 004 TRUE FALSE FALSE FALSE\n 005 TRUE FALSE FALSE FALSE\n 006 TRUE FALSE FALSE FALSE\n 007 TRUE FALSE FALSE FALSE\n 008 TRUE FALSE FALSE FALSE\n 009 TRUE FALSE FALSE FALSE\n 010 FALSE FALSE FALSE FALSE\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nRefinement ----------------------------------------------\nsetting up a move map\nsetting all backbone movement to true, and residue 10 to false\noutputting movemap\nmover: ClassicFragmentMover, 3mer\nCreating standard score function with patch and scoring\nmover: SmallMover\nMover name: Small, Mover type: SmallMover, Mover current tag:NoTag\nMax angle for helices (H): 0\nMax angle for strands (E): 5\nMax angle for loops (L): 50\nTemperature factor (kT): 0.5\nNumber of moves: 1\n\nmover: ShearMover\nMover name: Shear, Mover type: ShearMover, Mover current tag:NoTag\nMax angle for helices (H): 0\nMax angle for strands (E): 50\nMax angle for loops (L): 6\nTemperature factor (kT): 0.5\nNumber of moves: 1\n\nmover: MinMover\nmover: MonteCarlo\nprotocols.moves.MonteCarlo:\n\"Temperature\" (kT): 1\nTotal Trials: 4\nLowest Score: 23.6488\nLast Accepted Score: 23.6488\nlast_accept = 23.6488\n\nmover: SequenceMover\nmover: TrialMover\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments\ncore.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.230331 seconds to load from binary\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 23.6488 23.6488\nprotocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820\nprotocols.moves.MonteCarlo: MC: 1 23.6488 23.6488 23.6488 23.6488 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt\ncore.scoring.AtomVDW: Openning alternative vdw file: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/chemical/atom_type_sets/centroid_rot//min.txt\ncore.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN\nprotocols.TrialMover: Acceptance rate: 1\nprotocols.moves.MonteCarlo: MC: 1 22.6785 22.6785 22.6785 22.6785 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: ClassicFragmentM trials= 1; accepts= 1.0000; energy_drop/trial= -0.97029\nprotocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820\n\nFinished T400_Refinement in 0:00:07.923597", "state": "passed"}, "T500_Packing": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nPacking and Design ----------------------------------------------\nmover: PackRotamersMover\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tASP:NtermProteinFull\n2\tTRUE\tFALSE\tALA\n3\tTRUE\tFALSE\tILE\n4\tTRUE\tFALSE\tTHR\n5\tFALSE\tFALSE\t\n6\tTRUE\tFALSE\tHIS,HIS_D\n7\tTRUE\tFALSE\tSER\n8\tTRUE\tFALSE\tILE\n9\tTRUE\tFALSE\tLEU\n10\tTRUE\tFALSE\tASP\n11\tTRUE\tFALSE\tTRP\n12\tTRUE\tFALSE\tILE\n13\tTRUE\tFALSE\tGLU\n14\tTRUE\tFALSE\tASP\n15\tTRUE\tFALSE\tASN\n16\tTRUE\tFALSE\tLEU\n17\tTRUE\tFALSE\tGLU\n18\tTRUE\tFALSE\tSER\n19\tTRUE\tFALSE\tPRO\n20\tTRUE\tFALSE\tLEU\n21\tTRUE\tFALSE\tSER\n22\tTRUE\tFALSE\tLEU\n23\tTRUE\tFALSE\tGLU\n24\tTRUE\tFALSE\tLYS\n25\tTRUE\tFALSE\tVAL\n26\tTRUE\tFALSE\tSER\n27\tTRUE\tFALSE\tGLU\n28\tTRUE\tFALSE\tARG\n29\tTRUE\tFALSE\tSER\n30\tTRUE\tFALSE\tGLY\n31\tTRUE\tFALSE\tTYR\n32\tTRUE\tFALSE\tSER\n33\tTRUE\tFALSE\tLYS\n34\tTRUE\tFALSE\tTRP\n35\tTRUE\tFALSE\tHIS,HIS_D\n36\tTRUE\tFALSE\tLEU\n37\tTRUE\tFALSE\tGLN\n38\tTRUE\tFALSE\tARG\n39\tTRUE\tFALSE\tMET\n40\tTRUE\tFALSE\tPHE\n41\tTRUE\tFALSE\tLYS\n42\tTRUE\tFALSE\tLYS\n43\tTRUE\tFALSE\tGLU\n44\tTRUE\tFALSE\tTHR\n45\tTRUE\tFALSE\tGLY\n46\tTRUE\tFALSE\tHIS,HIS_D\n47\tTRUE\tFALSE\tSER\n48\tTRUE\tFALSE\tLEU\n49\tTRUE\tFALSE\tGLY\n50\tTRUE\tFALSE\tGLN\n51\tTRUE\tFALSE\tTYR\n52\tTRUE\tFALSE\tILE\n53\tTRUE\tFALSE\tARG\n54\tTRUE\tFALSE\tSER\n55\tTRUE\tFALSE\tARG\n56\tTRUE\tFALSE\tLYS\n57\tTRUE\tFALSE\tMET\n58\tTRUE\tFALSE\tTHR\n59\tTRUE\tFALSE\tGLU\n60\tTRUE\tFALSE\tILE\n61\tTRUE\tFALSE\tALA\n62\tTRUE\tFALSE\tGLN\n63\tTRUE\tFALSE\tLYS\n64\tTRUE\tFALSE\tLEU\n65\tTRUE\tFALSE\tLYS\n66\tTRUE\tFALSE\tGLU\n67\tTRUE\tFALSE\tSER\n68\tTRUE\tFALSE\tASN\n69\tTRUE\tFALSE\tGLU\n70\tTRUE\tFALSE\tPRO\n71\tTRUE\tFALSE\tILE\n72\tTRUE\tFALSE\tLEU\n73\tTRUE\tFALSE\tTYR\n74\tTRUE\tFALSE\tLEU\n75\tTRUE\tFALSE\tALA\n76\tTRUE\tFALSE\tGLU\n77\tTRUE\tFALSE\tARG\n78\tTRUE\tFALSE\tTYR\n79\tTRUE\tFALSE\tGLY\n80\tTRUE\tFALSE\tPHE\n81\tTRUE\tFALSE\tGLU\n82\tTRUE\tFALSE\tSER\n83\tTRUE\tFALSE\tGLN\n84\tTRUE\tFALSE\tGLN\n85\tTRUE\tFALSE\tTHR\n86\tTRUE\tFALSE\tLEU\n87\tTRUE\tFALSE\tTHR\n88\tTRUE\tFALSE\tARG\n89\tTRUE\tFALSE\tTHR\n90\tTRUE\tFALSE\tPHE\n91\tTRUE\tFALSE\tLYS\n92\tTRUE\tFALSE\tASN\n93\tTRUE\tFALSE\tTYR\n94\tTRUE\tFALSE\tPHE\n95\tTRUE\tFALSE\tASP\n96\tTRUE\tFALSE\tVAL\n97\tTRUE\tFALSE\tPRO\n98\tTRUE\tFALSE\tPRO\n99\tTRUE\tFALSE\tHIS,HIS_D\n100\tTRUE\tFALSE\tLYS\n101\tTRUE\tFALSE\tTYR\n102\tTRUE\tFALSE\tARG\n103\tTRUE\tFALSE\tMET\n104\tTRUE\tFALSE\tTHR\n105\tTRUE\tFALSE\tASN\n106\tTRUE\tFALSE\tMET\n107\tTRUE\tFALSE\tGLN\n108\tTRUE\tFALSE\tGLY\n109\tTRUE\tFALSE\tGLU\n110\tTRUE\tFALSE\tSER\n111\tTRUE\tFALSE\tARG\n112\tTRUE\tFALSE\tPHE\n113\tTRUE\tFALSE\tLEU\n114\tTRUE\tFALSE\tHIS,HIS_D\n115\tTRUE\tFALSE\tPRO\n116\tTRUE\tFALSE\tLEU:CtermProteinFull\n\nMover name: PackRotamersMover, Mover type: PackRotamersMover, Mover current tag:NoTag\nScore function: ref2015\n\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tTRUE\tALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n2\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n3\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n4\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n5\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n6\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n7\tFALSE\tFALSE\t\n8\tFALSE\tFALSE\t\n9\tFALSE\tFALSE\t\n10\tFALSE\tFALSE\t\n11\tFALSE\tFALSE\t\n12\tFALSE\tFALSE\t\n13\tFALSE\tFALSE\t\n14\tFALSE\tFALSE\t\n15\tFALSE\tFALSE\t\n16\tFALSE\tFALSE\t\n17\tFALSE\tFALSE\t\n18\tFALSE\tFALSE\t\n19\tFALSE\tFALSE\t\n20\tFALSE\tFALSE\t\n21\tFALSE\tFALSE\t\n22\tFALSE\tFALSE\t\n23\tFALSE\tFALSE\t\n24\tFALSE\tFALSE\t\n25\tFALSE\tFALSE\t\n26\tFALSE\tFALSE\t\n27\tFALSE\tFALSE\t\n28\tFALSE\tFALSE\t\n29\tFALSE\tFALSE\t\n30\tFALSE\tFALSE\t\n31\tFALSE\tFALSE\t\n32\tFALSE\tFALSE\t\n33\tFALSE\tFALSE\t\n34\tFALSE\tFALSE\t\n35\tFALSE\tFALSE\t\n36\tFALSE\tFALSE\t\n37\tFALSE\tFALSE\t\n38\tFALSE\tFALSE\t\n39\tFALSE\tFALSE\t\n40\tFALSE\tFALSE\t\n41\tFALSE\tFALSE\t\n42\tFALSE\tFALSE\t\n43\tFALSE\tFALSE\t\n44\tFALSE\tFALSE\t\n45\tFALSE\tFALSE\t\n46\tFALSE\tFALSE\t\n47\tFALSE\tFALSE\t\n48\tFALSE\tFALSE\t\n49\tFALSE\tFALSE\t\n50\tFALSE\tFALSE\t\n51\tFALSE\tFALSE\t\n52\tFALSE\tFALSE\t\n53\tFALSE\tFALSE\t\n54\tFALSE\tFALSE\t\n55\tFALSE\tFALSE\t\n56\tFALSE\tFALSE\t\n57\tFALSE\tFALSE\t\n58\tFALSE\tFALSE\t\n59\tFALSE\tFALSE\t\n60\tFALSE\tFALSE\t\n61\tFALSE\tFALSE\t\n62\tFALSE\tFALSE\t\n63\tFALSE\tFALSE\t\n64\tFALSE\tFALSE\t\n65\tFALSE\tFALSE\t\n66\tFALSE\tFALSE\t\n67\tFALSE\tFALSE\t\n68\tFALSE\tFALSE\t\n69\tFALSE\tFALSE\t\n70\tFALSE\tFALSE\t\n71\tFALSE\tFALSE\t\n72\tFALSE\tFALSE\t\n73\tFALSE\tFALSE\t\n74\tFALSE\tFALSE\t\n75\tFALSE\tFALSE\t\n76\tFALSE\tFALSE\t\n77\tFALSE\tFALSE\t\n78\tFALSE\tFALSE\t\n79\tFALSE\tFALSE\t\n80\tFALSE\tFALSE\t\n81\tFALSE\tFALSE\t\n82\tFALSE\tFALSE\t\n83\tFALSE\tFALSE\t\n84\tFALSE\tFALSE\t\n85\tFALSE\tFALSE\t\n86\tFALSE\tFALSE\t\n87\tFALSE\tFALSE\t\n88\tFALSE\tFALSE\t\n89\tFALSE\tFALSE\t\n90\tFALSE\tFALSE\t\n91\tFALSE\tFALSE\t\n92\tFALSE\tFALSE\t\n93\tFALSE\tFALSE\t\n94\tFALSE\tFALSE\t\n95\tFALSE\tFALSE\t\n96\tFALSE\tFALSE\t\n97\tFALSE\tFALSE\t\n98\tFALSE\tFALSE\t\n99\tFALSE\tFALSE\t\n100\tFALSE\tFALSE\t\n101\tFALSE\tFALSE\t\n102\tFALSE\tFALSE\t\n103\tFALSE\tFALSE\t\n104\tFALSE\tFALSE\t\n105\tFALSE\tFALSE\t\n106\tFALSE\tFALSE\t\n107\tFALSE\tFALSE\t\n108\tFALSE\tFALSE\t\n109\tFALSE\tFALSE\t\n110\tFALSE\tFALSE\t\n111\tFALSE\tFALSE\t\n112\tFALSE\tFALSE\t\n113\tFALSE\tFALSE\t\n114\tFALSE\tFALSE\t\n115\tFALSE\tFALSE\t\n116\tFALSE\tFALSE\t\n\nGGGG\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.15048 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.245669 seconds to load from binary\ncore.pack.pack_rotamers: built 2848 rotamers at 115 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 1023 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 2822 rotamers at 115 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.minimization_packing.PackRotamersMover: [ WARNING ] undefined ScoreFunction -- creating a default one\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 4 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\n\nFinished T500_Packing in 0:00:12.203178", "state": "passed"}, "T600_Docking": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.00117 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.240812 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.025153 seconds.\nprotocols.moves.RigidBodyMover: Spin: Jump (before): RT -0.389931 0.810342 -0.437379 -0.892411 -0.449663 -0.0375013 -0.227062 0.375699 0.898495 -12.6138 -39.3747 8.5794 \nprotocols.moves.RigidBodyMover: Spin: Rot (before): 40.7713 27.6633 9.48574\nprotocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.106732 -0.00891842 -0.994248 -0.993895 0.0271569 -0.106937 0.0279544 0.999591 -0.00596546 -11.6523 -39.1223 10.5884 \nprotocols.moves.RigidBodyMover: Spin: Rot (after): 40.7713 27.6633 9.48574\nprotocols.moves.RigidBodyMover: Spin: ---\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nprotocols.docking.DockingInitialPerturbation: sliding into contact\nprotocols.docking.DockingInitialPerturbation: Moving away\nprotocols.docking.DockingInitialPerturbation: Moving together\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.36\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.16\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.2\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.22\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.22\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.12\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.Doc\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nDocking ----------------------------------------------------\nkingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.24\n\nFinished T600_Docking in 0:00:10.154493", "state": "passed"}, "T650_LoopsKIC": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nLOOP start: 145 stop: 155 cut: 150 size: 11 skip rate: 0 extended?: False\n\nFOLD_TREE EDGE 1 144 -1 EDGE 144 150 -1 EDGE 144 156 1 EDGE 156 151 -1 EDGE 156 164 -1 \nsetting up movers\nbuilding random loop conformation with ideal bond lengths, bond angles,\nand omega angles using KIC\n attempt 0...succeeded.\ncentroid stage loop KIC remodeling\ncentroid stage loop rmsd to starting loop: 6.509848\nhigh-res KIC refinement\noutputting decoy .test_kic.pdb\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -run:test_cycles True -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.15788 seconds.\ncore.import_pose.import_pose: File '../test/data/2cpl_min.pdb' automatically determined to be of type PDB\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nprotocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 144 -1 EDGE 144 150 -1 EDGE 144 156 1 EDGE 156 151 -1 EDGE 156 164 -1 \ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.018925 seconds.\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 3\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.223061 seconds to load from binary\ncore.pack.pack_rotamers: built 1908 rotamers at 164 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine init temp: 1.5\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine final temp: 0.5\ncore.pack.task: Packer task: initialize from command line() \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: Not designing\ncore.pack.pack_rotamers: built 1123 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -368.432 -368.432\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 1 -368.432\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 1/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.2083\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -378.23\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.21809\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -385.696\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 2/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 3/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.22069\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -385.961\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.23099\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -388.721\ncore.pack.pack_rotamers: built 1010 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -388.751\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -388.752 -388.752\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -388.752\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 2 -387.79\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 1/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.23853\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -387.783\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 2/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.39798\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -386.913\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 3/3 \ncore.pack.pack_rotamers: built 993 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -386.95\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -386.953 -387.79\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -386.953\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 3 -386.828\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 1/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 3.00362\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -390.438\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 2/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 3/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.97232\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -390.652\ncore.pack.pack_rotamers: built 1018 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -391.58\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -391.593 -391.593\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -391.593\nprotocols.moves.TrialCounter: kic_refine_r1 trials= 8; accepts= 0.6250; energy_drop/trial= -1.59952\nprotocols.moves.TrialCounter: kic_refine_r2 trials= 9; accepts= 0.3333; energy_drop/trial= -1.16001\nprotocols.moves.TrialCounter: repack trials= 4; accepts= 1.0000; energy_drop/trial= -59.86967\n\nFinished T650_LoopsKIC in 0:00:18.817540", "state": "passed"}, "T660_LoopBuilding": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.11142 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nprotocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.255818 seconds to load from binary\nprotocols.loops.loops_main: Added cutpoint variant to residue 75\nprotocols.loops.loops_main: Added cutpoint variant to residue 76\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1201 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 649.218 649.218\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 1 649.218\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 585.944 585.944\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.737 583.737\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.328 583.328\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.519 583.328\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.189 583.189\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.669 582.669\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.527 582.669\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.69 582.669\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.412 582.412\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.412 582.412\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.663 581.663\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.111 581.111\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.071 581.071\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.612 580.612\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.696 580.612\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.19 580.19\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.842 579.842\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.628 579.628\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.232 579.232\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.633 579.232\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1088 rotamers at 43 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.633 579.232\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 2 579.69\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.214 579.69\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.045 579.69\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.954 579.69\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.025 579.69\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.806 579.69\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.806 579.69\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.642 579.642\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.666 579.642\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.768 579.642\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.759 579.642\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.459 579.459\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.164 579.164\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.243 579.164\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.184 579.164\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.189 579.164\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.137 579.137\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.237 579.137\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.145 579.137\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.342 579.137\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.151 579.137\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1076 rotamers at 43 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.15 579.137\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 3 579.284\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.224 579.224\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.224 579.224\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.218 579.218\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.907 578.907\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.811 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.811 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.014 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.44 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.44 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.928 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.847 578.811\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.708 578.708\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.352 578.352\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.352 578.352\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.321 578.321\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.233 578.233\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.284 578.233\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.229 578.229\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 3/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.234 578.229\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.226 578.226\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1070 rotamers at 43 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.226 578.226\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 4 578.348\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.348 578.348\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.52 578.348\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.797 578.348\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.573 578.348\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.066 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.108 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.108 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.256 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.793 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.649 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.499 578.066\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.972 577.972\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.821 577.821\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.577\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.468 577.468\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 4/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.577 577.468\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.021 577.468\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1065 rotamers at 43 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.021 577.468\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 5 577.556\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.269 577.556\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.76 577.556\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.76 577.556\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.76 577.556\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.895 577.556\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.474 577.474\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.474 577.474\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.345 577.345\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.345 577.345\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.604 577.345\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.396 577.345\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.216 577.216\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.274 577.216\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.299 577.216\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for S\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nLoop building --------------------------------------------------\nFOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 \nmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.252 577.216\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.273 577.216\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.273 577.216\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.191 577.191\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.295 577.191\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.306 577.191\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1086 rotamers at 43 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 577.306 577.191\nprotocols.moves.TrialCounter: repack trials= 6; accepts= 1.0000; energy_drop/trial= -50.02512\nprotocols.moves.TrialCounter: shear_ccd_min trials= 50; accepts= 0.8600; energy_drop/trial= -0.15222\nprotocols.moves.TrialCounter: small_ccd_min trials= 50; accepts= 0.8200; energy_drop/trial= -1.28296\n\nFinished T660_LoopBuilding in 0:00:52.414121", "state": "passed"}, "T700_FoldTree": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nFold tree --------------------------------------------------\nFOLD_TREE EDGE 1 116 -1 \nFOLD_TREE EDGE 1 30 -1 EDGE 30 40 -1 EDGE 30 50 1 EDGE 50 116 -1 EDGE 50 41 -1 \n116 5 1\nFOLD_TREE EDGE 1 30 -1 EDGE 30 40 -1 EDGE 30 50 1 EDGE 50 41 -1 EDGE 50 116 -1 \nFOLD_TREE \ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.12931 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n\nFinished T700_FoldTree in 0:00:03.877605", "state": "passed"}, "T800_ClassicRelax": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ntesting ClassicRelax\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.07082 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nprotocols.relax.ClassicRelax: Setting up default relax setting\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.22693 seconds to load from binary\nprotocols.relax.ClassicRelax: \nprotocols.relax.ClassicRelax: \nprotocols.relax.ClassicRelax: ===================================================================\nprotocols.relax.ClassicRelax: Stage 1 \nprotocols.relax.ClassicRelax: Ramping repulsives with 3 outer cycles and 3 inner cycles\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 4003 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 3603 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 3138 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 3063 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.relax.ClassicRelax: \nprotocols.relax.ClassicRelax: ===================================================================\nprotocols.relax.ClassicRelax: Stage 2 \nprotocols.relax.ClassicRelax: Mainmintrial for 10 with a full repack every 100 cycles\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.relax.ClassicRelax: \nprotocols.relax.ClassicRelax: ===================================================================\nprotocols.relax.ClassicRelax: Stage 3 \nprotocols.relax.ClassicRelax: Mainmintrial for 10\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.relax.ClassicRelax: \n\nFinished T800_ClassicRelax in 0:00:40.261225", "state": "passed"}, "T850_SubClassing": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\nBase::Base()\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nA.__init__...\nPyValue.__init__...\nA.foo_int(1)\nA.foo_value(wrong...)\nA.foo_string(qwerty)\nNew Value[1]: A.foo_value! \n\nA.foo_value(wrong...)\nNew Value[2]: A.foo_value! \n\nA.foo_value_sp(wrong...)\nNew Value[3]: A.foo_value_sp! \n\nA.foo_int(1)\nA.foo_value(wrong...)\nA.foo_string(qwerty)\nNew Value[4]: A.foo_value! \n\nA.foo_int(1)\nA.foo_value(wrong...)\nA.foo_string(qwerty)\nNew Value[5]: A.foo_value! \n\nrosetta.utility.py.OverloadTest Test -----------------------\nOverloadTest::self_test_virtual_p...\n Calling test(Value *v)...\n Calling test(Value *v)... Done!\nOverloadTest::self_test_virtual_p... Done!\nOverloadTest::self_test_virtual_ref...\n Calling test(Value &v)...\n Calling test(Value &v)... Done!\nOverloadTest::self_test_virtual_ref... Done!\nPyOverloadTest Test -----------------------------------------\nOverloadTest::self_test_virtual_p...\n Calling test(Value *v)...\n Calling test(Value *v)... Done!\nOverloadTest::self_test_virtual_p... Done!\nOverloadTest::self_pure_test_virtual_p...\n Calling pure_test(Value *v)...\n Calling pure_test(Value *v)... Done!\nOverloadTest::self_pure_test_virtual_p... Done!\nOverloadTest::self_test_virtual_ref...\n Calling test(Value &v)...\n Calling test(Value &v)... Done!\nOverloadTest::self_test_virtual_ref... Done!\nOverloadTest::self_pure_test_virtual_ref...\n Calling pure_test(Value &v)...\n Calling pure_test(Value &v)... Done!\nOverloadTest::self_pure_test_virtual_ref... Done!\nPyOverloadTest.test_p(Value('unknown') )\nPyOverloadTest.pure_test_p(Value('unknown') )\nPyOverloadTest.test_ref(Value('unknown') )\nPyOverloadTest.pure_test_ref(Value('unknown') )\nMy_New_Mover.__init__...\nMy_New_Mover.apply: <class 'pyrosetta.rosetta.core.pose.Pose'>\nThis My_New_Mover apply...\nOld phi=0.0, new phi=1.54\nMyNewCI1B::__init__!\n---------------------------------------------\nScore: 232.0\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.09352 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nValue destructor! [A.foo_value_sp!]\nValue destructor! [A.foo_value!]\nValue destructor! [unknown]\nValue destructor! [unknown]\n\nFinished T850_SubClassing in 0:00:03.790342", "state": "passed"}, "T860_SubClassing_EnergyMethods": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n---------------------------------------------\nMyCI1B_Method Score: 232.0\nprotocols.moves.MonteCarlo:\n\"Temperature\" (kT): 1\nTotal Trials: 0\nLowest Score: 232\nLast Accepted Score: 232\nlast_accept = 232\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.04631 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n\nFinished T860_SubClassing_EnergyMethods in 0:00:03.881239", "state": "passed"}, "T870_SubClassing_EnergyMethods2": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n---------------------------------------------\nCI1B_Method Score: 232.0\n---------------------------------------------\nCI2B_Method Score: 525.0\n---------------------------------------------\nCD2B_Method Score: 525.0\n\n\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.11352 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/test/T870_SubClassing_EnergyMethods2.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.core.scoring.methods import ContextIndependentOneBodyEnergy, ContextIndependentTwoBodyEnergy, ContextDependentTwoBodyEnergy\n\nFinished T870_SubClassing_EnergyMethods2 in 0:00:03.819345", "state": "passed"}, "T880_Other": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\ntesting ligand modeling\ntesting DNA modeling\nDone!\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.05196 seconds.\ncore.import_pose.import_pose: File '../test/data/ligand_test.pdb' automatically determined to be of type PDB\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.229337 seconds to load from binary\ncore.import_pose.import_pose: File '../test/data/dna_test.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name O5* to O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name C5* to C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Number of nucleic acid residue fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: -12 C DG GUA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: P \ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C4'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 164 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 166 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 167 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 169 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 170 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 172 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 173 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 174 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:UpperRNA:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 175 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE:LowerDNA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 177 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 181 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 182 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 183 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 184 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 185 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 186 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT:UpperDNA\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for OP1 and OP2 for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 161\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N9 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N7 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C8 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: Connecting residues: 162 ( GUA:LowerDNA:VirtualDNAPhosphate ) and 163 ( CYT ) at atoms O3' and P \ncore.conformation.Conformation: with mutual distances: 0.293633 and 0.00610344\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 163 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 164 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 165 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 166 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 167 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 168 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 169 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 170 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 171 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 172 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 173 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 174 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 175 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 176 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 177 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 178 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 179 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 181 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 182 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 183 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 184 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 185 atom 2H2' (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 12 atom name N9 \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished T880_Other in 0:00:07.023528", "state": "passed"}, "T900_distributed": {"log": "Unsupported python version for pyrosetta.distributed: sys.version_info(major=3, minor=10, micro=10, releaselevel='final', serial=0)\n\nFinished T900_distributed in 0:00:00.033965", "state": "passed"}, "Workshop2test": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nPDB file name: ../test/data/workshops/1YY8.clean.pdb\nTotal residues: 868\nSequence: DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS\nFold tree:\nFOLD_TREE EDGE 1 213 -1 EDGE 1 214 1 EDGE 214 434 -1 EDGE 1 435 2 EDGE 435 647 -1 EDGE 1 648 3 EDGE 648 868 -1 \nDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS\nProtein has 868 residues.\nGLY\nC\n66\n100\n25 A \n1 9 17 25 33 41 49 57 65 73 \nDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVES\nLLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLH\n\n\n81 89 97 105 113 121 129 137 145 153 \nEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ\nHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLLEEEEEELLEELLLLEE\n\n\n161 169 177 185 193 201 209 217 225 233 \nESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGF\nEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEELLLLLLLEEEEEELLLLLEEEELLLEEELLLLLEEEEEEEELL\n\n\n241 249 257 265 273 281 289 297 305 313 \nSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFA\nLLLLLLEEEEEELLLLLEEEEEEELLLLLEEELHHHLLLEEEEEELLLLEEEEEELLLLHHHLEEEEEEEELLLLLLLEE\n\n\n321 329 337 345 353 361 369 377 385 393 \nYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV\nEELLLEEEEELLLLLELLEEEEELLLHHHEEHHEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEE\n\n\n401 409 417 425 433 441 449 457 465 473 \nVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRL\nEEEEHHHLLLLLLEEEEEEHHHLEEEEEELLLLLLLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEE\n\n\n481 489 497 505 513 521 529 537 545 553 \nLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLK\nEEELLLEELLLLLLLEEEEEELLEEEEEELLLLHHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHH\n\n\n561 569 577 585 593 601 609 617 625 633 \nSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVT\nHLEEEEEEEEEEEELLLEEEEEEELLEEELLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEEELLLLLLEE\n\n\n641 649 657 665 673 681 689 697 705 713 \nKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDN\nEEEELLLLLEEEELLLEEELLLLLEEEEEEEELLLLLLLLEEEEEELLLLLEEEEEEELLLLLEEELHHHLLLEEEEEEL\n\n\n721 729 737 745 753 761 769 777 785 793 \nSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP\nLLLEEEEEELLLLHHHLEEEEEEEELLLLLLLEEEELLLEEEEELLLLLELLEEEEELLLHHHEEHHEEEEEEEEEEEEL\n\n\n801 809 817 825 833 841 849 857 865 \nEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS\nLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHHHLLLLEEEEEEHHHLEEEEEELLLLL\n\n\n-112.78988533697459\n119.19490144825456\n-59.969147488992036\n1.4632323807242649\n1.5092534578393384\n<bound method PyCapsule.norm of <pyrosetta.rosetta.numeric.xyzVector_double_t object at 0x111f46d30>>\n1.887434528690777\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.01634 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.217347 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished Workshop2test in 0:00:07.402150", "state": "passed"}, "Workshop3test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.02147 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/6Q21.clean.pdb' automatically determined to be of type PDB\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.203326 seconds to load from binary\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 1.000 -4241.897 -4241.897\n fa_rep 0.550 4336.454 2385.050\n fa_sol 1.000 2798.424 2798.424\n fa_intra_rep 0.005 3035.687 15.178\n fa_intra_sol_xover4 1.000 180.944 180.944\n lk_ball_wtd 1.000 -56.460 -56.460\n fa_elec 1.000 -933.702 -933.702\n pro_close 1.250 270.565 338.206\n hbond_sr_bb 1.000 -181.224 -181.224\n hbond_lr_bb 1.000 -130.586 -130.586\n hbond_bb_sc 1.000 -58.168 -58.168\n hbond_sc 1.000 -38.850 -38.850\n dslf_fa13 1.250 0.000 0.000\n omega 0.400 149.145 59.658\n fa_dun 0.700 4635.733 3245.013\n p_aa_pp 0.600 -101.427 -60.856\n yhh_planarity 0.625 0.000 0.000\n ref 1.000 188.455 188.455\n rama_prepro 0.450 591.830 266.324\n---------------------------------------------------\n Total weighted score: 3775.512\ncore.scoring.Energies: E fa_atr fa_rep fa_sol fa_intra_repfa_intra_sol_x lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref rama_prepro\ncore.scoring.Energies: E(i) 24 -7.40 19.03 2.94 8.76 0.09 -0.11 -0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.12 2.68 0.06 0.00 2.30 3.58\ncore.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 162 GLU OE1 1.87 152.3 115.2 157.1 1.000 -1.850\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 165 GLN OE1 1.59 159.1 136.2 147.7 0.859 -1.567\ncore.scoring.hbonds.HBondSet: #A 52 LEU N A 2 THR O 1.59 171.0 149.6 134.7 1.000 -0.439\ncore.scoring.hbonds.HBondSet: #A 2 THR N A 50 THR O 2.01 158.3 155.0 -175.7 1.000 -1.342\ncore.scoring.hbonds.HBondSet: #A 4 TYR N A 52 LEU O 1.71 146.0 157.4 151.1 1.000 -0.468\ncore.scoring.hbonds.HBondSet: #A 54 ASP N A 4 TYR O 1.72 151.1 150.2 49.0 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #A 5 LYS N A 76 GLU OE1 1.52 175.1 149.4 13.9 0.765 -1.324\ncore.scoring.hbonds.HBondSet: #A 76 GLU N A 5 LYS O 1.97 142.0 123.6 -73.8 1.000 -0.616\ncore.scoring.hbonds.HBondSet: #A 77 GLY N A 5 LYS O 2.16 141.0 146.4 -155.0 1.000 -0.989\ncore.scoring.hbonds.HBondSet: #A 6 LEU N A 54 ASP O 1.88 169.2 151.8 102.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #A 56 LEU N A 6 LEU O 2.05 163.6 163.5 167.1 1.000 -1.200\ncore.scoring.hbonds.HBondSet: #A 7 VAL N A 77 GLY O 1.65 159.9 148.6 -140.0 1.000 -0.669\ncore.scoring.hbonds.HBondSet: #A 8 VAL N A 56 LEU O 2.14 166.5 145.2 73.7 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 8 VAL O 2.66 140.8 137.3 32.0 1.000 -0.139\ncore.scoring.hbonds.HBondSet: #A 81 VAL N A 9 VAL O 1.76 166.8 144.1 -124.3 1.000 -0.996\ncore.scoring.hbonds.HBondSet: #A 9 VAL N A 79 LEU O 1.98 138.4 151.4 57.5 1.000 -0.592\ncore.scoring.hbonds.HBondSet: #A 14 VAL N A 11 ALA O 1.88 154.8 146.6 -154.7 1.000 -1.324\ncore.scoring.hbonds.HBondSet: #A 117 LYS NZ A 13 GLY O 2.09 158.9 168.0 43.3 0.929 -0.307\ncore.scoring.hbonds.HBondSet: #A 116 ASN ND2A 14 VAL O 2.17 167.3 134.9 147.9 1.000 -1.433\ncore.scoring.hbonds.HBondSet: #A 19 LEU N A 15 GLY O 1.86 152.2 155.7 -122.2 1.000 -0.811\ncore.scoring.hbonds.HBondSet: #A 20 THR N A 16 LYS O 1.90 177.7 161.6 -167.9 1.000 -1.327\ncore.scoring.hbonds.HBondSet: #A 21 ILE N A 17 SER O 1.81 151.9 161.2 83.6 1.000 -0.613\ncore.scoring.hbonds.HBondSet: #A 17 SER OG A 57 ASP OD2 1.82 126.8 115.0 -166.4 1.000 -0.827\ncore.scoring.hbonds.HBondSet: #A 22 GLN N A 18 ALA O 2.31 140.8 122.1 -104.6 1.000 -0.323\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 19 LEU O 2.28 137.6 137.1 -174.9 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 20 THR O 1.97 123.1 112.5 -78.8 1.000 -0.055\ncore.scoring.hbonds.HBondSet: #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979\ncore.scoring.hbonds.HBondSet: #A 25 GLN N A 21 ILE O 2.24 105.4 127.6 -17.1 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 22 GLN O 1.69 156.8 124.3 126.5 0.859 -0.895\ncore.scoring.hbonds.HBondSet: #A 30 ASP N A 31 GLU OE2 1.95 148.8 110.5 52.5 0.318 -1.124\ncore.scoring.hbonds.HBondSet: #A 57 ASP N A 38 ASP O 2.02 149.5 176.9 -58.1 1.000 -0.727\ncore.scoring.hbonds.HBondSet: #A 40 TYR N A 55 ILE O 2.06 133.0 125.1 62.1 1.000 -0.543\ncore.scoring.hbonds.HBondSet: #A 55 ILE N A 40 TYR O 1.69 157.5 167.5 -58.5 1.000 -0.451\ncore.scoring.hbonds.HBondSet: #A 42 LYS N A 53 LEU O 2.02 144.4 129.4 31.9 1.000 -1.371\ncore.scoring.hbonds.HBondSet: #A 53 LEU N A 42 LYS O 1.74 153.8 165.7 -34.7 1.000 -0.598\ncore.scoring.hbonds.HBondSet: #A 43 GLN NE2B 141 TYR O 1.70 166.6 150.3 33.2 0.859 -1.175\ncore.scoring.hbonds.HBondSet: #B 141 TYR N A 43 GLN OE1 2.24 131.2 99.3 -167.7 0.859 -0.219\ncore.scoring.hbonds.HBondSet: #A 44 VAL N A 51 CYS O 1.71 163.4 149.6 -1.3 1.000 -1.165\ncore.scoring.hbonds.HBondSet: #A 46 ILE N A 49 GLU O 2.07 141.6 134.8 -34.7 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #A 49 GLU N A 46 ILE O 2.22 146.3 99.6 95.0 1.000 -0.222\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD1 2.30 127.4 91.6 172.3 0.718 -0.063\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD2 2.37 163.9 86.4 -172.5 0.718 -0.412\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH1A 47 ASP OD2 1.48 142.3 122.9 -33.8 0.671 -0.468\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH2A 47 ASP OD2 1.87 128.8 120.1 73.7 0.671 -0.154\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH1A 49 GLU OE2 1.85 136.1 126.0 132.0 0.624 -0.645\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH2A 49 GLU OE2 2.28 126.2 161.1 -104.1 0.624 -0.007\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 56 LEU O 2.50 117.5 111.9 -148.7 1.000 -0.051\ncore.scoring.hbonds.HBondSet: #A 65 SER N A 63 GLU OE1 1.63 154.5 118.5 115.9 0.224 -0.884\ncore.scoring.hbonds.HBondSet: #A 68 ARG NH2A 96 TYR OH 1.81 164.5 113.9 -150.2 0.788 -1.692\ncore.scoring.hbonds.HBondSet: #A 74 THR OG1A 71 TYR O 2.00 159.3 114.5 -39.3 0.576 -0.378\ncore.scoring.hbonds.HBondSet: #A 71 TYR N A 72 MET O 2.18 108.7 111.7 7.3 1.000 -0.617\ncore.scoring.hbonds.HBondSet: #A 75 GLY N A 71 TYR O 1.64 137.5 150.1 -159.0 1.000 -0.191\ncore.scoring.hbonds.HBondSet: #A 104 LYS NZ A 75 GLY O 1.73 151.1 175.2 27.0 0.788 -0.427\ncore.scoring.hbonds.HBondSet: #A 112 VAL N A 78 PHE O 2.25 148.8 157.4 173.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 78 PHE N A 110 PRO O 2.01 158.7 153.2 -144.4 1.000 -1.242\ncore.scoring.hbonds.HBondSet: #A 80 CYS N A 112 VAL O 2.27 143.1 149.0 68.7 1.000 -0.434\ncore.scoring.hbonds.HBondSet: #A 114 VAL N A 80 CYS O 2.23 169.9 156.5 101.6 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 116 ASN N A 82 PHE O 1.76 152.5 166.5 -98.5 1.000 -0.518\ncore.scoring.hbonds.HBondSet: #A 82 PHE N A 114 VAL O 2.14 145.0 155.1 -96.1 1.000 -0.561\ncore.scoring.hbonds.HBondSet: #A 86 ASN N A 83 ALA O 2.32 149.5 107.5 -109.9 1.000 -0.454\ncore.scoring.hbonds.HBondSet: #A 83 ALA N A 89 SER OG 1.92 159.9 113.0 146.0 1.000 -2.159\ncore.scoring.hbonds.HBondSet: #A 84 ILE N A 116 ASN O 2.25 158.9 161.3 -45.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 124 THR N A 84 ILE O 1.65 177.5 159.1 166.1 1.000 -0.788\ncore.scoring.hbonds.HBondSet: #A 88 LYS N A 86 ASN OD1 1.96 146.5 130.0 -97.6 0.600 -0.800\ncore.scoring.hbonds.HBondSet: #A 90 PHE N A 86 ASN O 2.39 155.4 153.6 -141.6 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #A 91 GLU N A 87 THR O 2.43 136.5 134.7 -143.4 1.000 -0.557\ncore.scoring.hbonds.HBondSet: #A 92 ASP N A 88 LYS O 2.28 145.5 141.1 -118.0 1.000 -0.589\ncore.scoring.hbonds.HBondSet: #A 96 TYR N A 92 ASP O 2.47 148.2 144.3 139.2 1.000 -0.571\ncore.scoring.hbonds.HBondSet: #A 95 GLN N A 92 ASP O 1.65 147.8 124.5 -102.5 1.000 -0.067\ncore.scoring.hbonds.HBondSet: #A 97 ARG N A 93 ILE O 2.13 156.0 164.2 -73.0 1.000 -0.838\ncore.scoring.hbonds.HBondSet: #A 98 GLU N A 94 HIS O 2.17 155.1 127.3 -111.1 1.000 -0.919\ncore.scoring.hbonds.HBondSet: #A 99 GLN N A 95 GLN O 2.20 147.3 151.5 -140.0 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #A 100 ILE N A 96 TYR O 2.07 160.1 159.6 177.7 1.000 -1.238\ncore.scoring.hbonds.HBondSet: #A 101 LYS N A 97 ARG O 2.17 173.1 164.2 -178.2 1.000 -1.217\ncore.scoring.hbonds.HBondSet: #A 102 ARG N A 98 GLU O 2.38 139.0 138.2 -136.4 1.000 -0.549\ncore.scoring.hbonds.HBondSet: #A 103 VAL N A 99 GLN O 1.71 166.8 162.3 -144.5 1.000 -0.762\ncore.scoring.hbonds.HBondSet: #A 104 LYS N A 100 ILE O 1.67 160.9 170.6 -154.6 1.000 -0.436\ncore.scoring.hbonds.HBondSet: #A 105 ASP N A 102 ARG O 2.25 143.4 93.6 -86.8 1.000 -0.002\ncore.scoring.hbonds.HBondSet: #A 108 ASP N A 106 SER OG 1.97 152.0 90.6 86.3 0.365 -1.113\ncore.scoring.hbonds.HBondSet: #A 113 LEU N A 140 PRO O 1.81 148.3 171.8 67.9 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #A 142 ILE N A 113 LEU O 1.79 150.9 160.0 151.3 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #A 115 GLY N A 142 ILE O 2.24 157.4 135.9 129.0 1.000 -1.120\ncore.scoring.hbonds.HBondSet: #A 144 THR N A 115 GLY O 2.13 162.0 119.4 101.2 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 116 ASN OD1 1.85 141.7 101.3 -66.8 1.000 -0.539\ncore.scoring.hbonds.HBondSet: #A 120 LEU N A 117 LYS O 1.95 172.9 143.4 -107.1 1.000 -1.171\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 144 THR O 2.01 106.8 129.9 -132.7 1.000 -0.125\ncore.scoring.hbonds.HBondSet: #A 118 CYS N A 144 THR O 1.90 170.5 123.4 123.6 1.000 -1.398\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 143 GLU OE2 1.95 158.1 107.0 -145.0 0.741 -1.215\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH2A 143 GLU OE1 1.63 171.8 119.9 158.6 0.741 -1.303\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 125 VAL O 2.02 173.1 148.1 -124.0 0.694 -1.007\ncore.scoring.hbonds.HBondSet: #A 130 ALA N A 126 GLU O 1.87 158.8 152.0 -177.9 1.000 -1.364\ncore.scoring.hbonds.HBondSet: #A 132 ASP N A 128 ARG O 2.21 150.7 138.4 -109.6 1.000 -0.724\ncore.scoring.hbonds.HBondSet: #A 133 LEU N A 129 GLN O 2.28 151.1 146.3 -142.0 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 134 ALA N A 130 ALA O 1.79 166.2 162.7 -178.5 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #A 135 ARG N A 131 GLN O 1.83 166.3 155.5 -99.9 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #A 136 SER N A 132 ASP O 1.78 156.7 145.2 -115.7 1.000 -0.779\ncore.scoring.hbonds.HBondSet: #A 137 TYR N A 133 LEU O 1.92 158.6 154.8 -155.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #A 138 GLY N A 134 ALA O 1.83 121.8 139.0 -163.6 1.000 -0.700\ncore.scoring.hbonds.HBondSet: #A 139 ILE N A 134 ALA O 2.24 163.7 126.8 83.5 1.000 -0.871\ncore.scoring.hbonds.HBondSet: #A 141 TYR OH A 143 GLU OE2 1.54 139.3 111.7 0.2 0.953 -1.165\ncore.scoring.hbonds.HBondSet: #A 141 TYR N C 43 GLN OE1 2.08 161.9 118.7 -172.1 0.835 -2.242\ncore.scoring.hbonds.HBondSet: #C 43 GLN NE2A 141 TYR O 2.33 146.4 124.9 79.1 0.835 -0.190\ncore.scoring.hbonds.HBondSet: #A 148 THR N A 145 SER OG 2.05 157.6 137.3 -91.6 0.694 -1.629\ncore.scoring.hbonds.HBondSet: #A 145 SER N A 150 GLN O 2.02 170.9 150.4 -53.6 1.000 -1.299\ncore.scoring.hbonds.HBondSet: #A 150 GLN N A 148 THR OG1 2.60 158.2 106.0 37.4 0.553 -0.009\ncore.scoring.hbonds.HBondSet: #A 152 VAL N A 149 ARG O 2.41 170.1 119.9 -103.6 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 153 GLU OE2 2.57 140.9 135.9 23.0 0.671 -0.460\ncore.scoring.hbonds.HBondSet: #A 155 ALA N A 151 GLY O 2.17 152.2 149.8 -130.5 1.000 -0.948\ncore.scoring.hbonds.HBondSet: #A 156 PHE N A 152 VAL O 2.47 167.0 144.2 -123.9 1.000 -0.728\ncore.scoring.hbonds.HBondSet: #A 157 TYR N A 153 GLU O 1.72 169.3 166.5 -179.4 1.000 -0.834\ncore.scoring.hbonds.HBondSet: #A 157 TYR OH A 153 GLU OE1 2.17 146.9 99.0 117.3 0.765 -0.012\ncore.scoring.hbonds.HBondSet: #A 158 THR N A 154 ASP O 1.89 147.3 139.5 -98.2 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #A 159 LEU N A 155 ALA O 2.17 148.5 137.9 -132.2 1.000 -1.027\ncore.scoring.hbonds.HBondSet: #A 160 VAL N A 156 PHE O 2.05 159.9 143.0 -132.0 1.000 -1.295\ncore.scoring.hbonds.HBondSet: #A 161 ARG N A 157 TYR O 1.81 160.4 153.3 -118.9 1.000 -0.892\ncore.scoring.hbonds.HBondSet: #A 162 GLU N A 158 THR O 2.08 152.2 148.4 -125.7 1.000 -0.984\ncore.scoring.hbonds.HBondSet: #A 163 ILE N A 159 LEU O 2.04 159.2 154.3 -135.6 1.000 -1.160\ncore.scoring.hbonds.HBondSet: #A 164 ARG N A 160 VAL O 1.82 170.5 164.7 -100.1 1.000 -0.943\ncore.scoring.hbonds.HBondSet: #A 165 GLN N A 161 ARG O 1.77 162.3 145.7 -126.0 1.000 -0.962\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 162 GLU OE2 1.52 173.9 111.2 -150.8 0.859 -1.532\ncore.scoring.hbonds.HBondSet: #A 166 HIS N A 162 GLU O 1.67 153.5 143.8 -117.4 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #A 167 LYS N A 163 ILE O 1.81 160.2 169.3 -164.8 1.000 -0.852\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 165 GLN OE1 1.68 168.3 116.6 -140.8 0.694 -1.841\ncore.scoring.hbonds.HBondSet: #A 168 LEU N A 165 GLN O 2.16 161.1 119.3 -109.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 167 LYS O 2.09 119.4 111.3 -127.2 1.000 -0.278\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 171 LEU O 2.31 134.6 103.8 72.2 1.000 -0.014\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 162 GLU OE2 1.78 162.3 101.4 -153.1 0.953 -1.514\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 165 GLN OE1 2.24 168.6 123.5 -111.6 0.741 -0.769\ncore.scoring.hbonds.HBondSet: #B 52 LEU N B 2 THR O 1.61 169.6 162.9 148.4 1.000 -0.412\ncore.scoring.hbonds.HBondSet: #B 2 THR N B 50 THR O 2.03 162.9 155.5 -160.6 1.000 -1.366\ncore.scoring.hbonds.HBondSet: #B 4 TYR N B 52 LEU O 1.80 164.8 167.3 95.8 1.000 -0.828\ncore.scoring.hbonds.HBondSet: #B 54 ASP N B 4 TYR O 1.94 154.4 155.9 57.8 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #B 4 TYR OH B 49 GLU OE1 1.84 151.6 105.5 143.8 0.812 -0.974\ncore.scoring.hbonds.HBondSet: #B 5 LYS N B 76 GLU OE1 1.53 174.9 152.7 -34.8 0.765 -1.099\ncore.scoring.hbonds.HBondSet: #B 76 GLU N B 5 LYS O 1.69 161.1 146.8 -26.4 1.000 -1.018\ncore.scoring.hbonds.HBondSet: #B 77 GLY N B 5 LYS O 2.40 143.5 155.6 146.2 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #B 6 LEU N B 54 ASP O 2.00 144.1 139.4 96.3 1.000 -0.600\ncore.scoring.hbonds.HBondSet: #B 56 LEU N B 6 LEU O 1.66 162.8 157.9 174.1 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #B 79 LEU N B 7 VAL O 1.74 157.3 152.8 147.5 1.000 -0.891\ncore.scoring.hbonds.HBondSet: #B 7 VAL N B 77 GLY O 2.02 174.4 161.6 166.4 1.000 -1.357\ncore.scoring.hbonds.HBondSet: #B 58 THR N B 8 VAL O 2.72 146.2 149.3 -11.1 1.000 -0.011\ncore.scoring.hbonds.HBondSet: #B 8 VAL N B 56 LEU O 1.97 177.7 162.1 69.5 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 9 VAL N B 79 LEU O 1.99 152.6 143.2 57.5 1.000 -1.020\ncore.scoring.hbonds.HBondSet: #B 81 VAL N B 9 VAL O 1.91 177.5 153.5 -123.6 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #B 14 VAL N B 11 ALA O 2.39 160.5 137.3 -127.2 1.000 -0.898\ncore.scoring.hbonds.HBondSet: #B 19 LEU N B 15 GLY O 1.91 147.7 148.4 -139.0 1.000 -0.998\ncore.scoring.hbonds.HBondSet: #B 20 THR N B 16 LYS O 1.82 178.0 165.1 -147.9 1.000 -1.102\ncore.scoring.hbonds.HBondSet: #B 21 ILE N B 17 SER O 1.94 143.6 134.8 -118.0 1.000 -0.775\ncore.scoring.hbonds.HBondSet: #B 17 SER OG B 57 ASP OD2 2.05 111.8 116.7 177.1 1.000 -0.366\ncore.scoring.hbonds.HBondSet: #B 22 GLN N B 18 ALA O 1.97 153.3 145.9 -100.8 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #B 23 LEU N B 19 LEU O 2.30 169.7 154.3 -159.7 1.000 -1.230\ncore.scoring.hbonds.HBondSet: #B 24 ILE N B 20 THR O 2.14 171.9 143.2 -132.6 1.000 -1.403\ncore.scoring.hbonds.HBondSet: #B 25 GLN N B 21 ILE O 1.99 147.2 133.1 -81.7 1.000 -0.687\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 21 ILE O 2.58 123.3 138.4 -158.7 1.000 -0.044\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 22 GLN O 1.79 133.6 118.3 -62.9 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #B 38 ASP N B 57 ASP O 1.85 160.4 146.8 -3.4 1.000 -1.515\ncore.scoring.hbonds.HBondSet: #B 57 ASP N B 38 ASP O 1.89 149.2 160.7 -105.2 1.000 -0.676\ncore.scoring.hbonds.HBondSet: #B 40 TYR N B 55 ILE O 2.11 143.2 150.5 52.1 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #B 55 ILE N B 40 TYR O 2.12 137.4 137.0 -91.8 1.000 -0.380\ncore.scoring.hbonds.HBondSet: #B 42 LYS N B 53 LEU O 1.91 134.3 138.2 49.9 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #B 44 VAL N B 51 CYS O 1.91 173.0 163.2 -19.0 1.000 -1.262\ncore.scoring.hbonds.HBondSet: #B 51 CYS N B 44 VAL O 1.70 159.6 163.0 112.3 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #B 46 ILE N B 49 GLU O 1.89 149.1 141.5 15.9 1.000 -1.413\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 46 ILE O 1.91 143.8 123.3 -75.0 0.835 -0.513\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD2 2.06 128.7 100.1 -167.7 0.718 -0.614\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD1 1.97 118.9 114.3 145.6 0.718 -0.498\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH1B 47 ASP OD2 1.52 144.2 128.2 -31.0 0.741 -0.595\ncore.scoring.hbonds.HBondSet: #B 164 ARG NE B 49 GLU OE1 2.22 142.9 142.9 -117.5 0.788 -0.542\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 49 GLU OE1 2.04 151.6 123.3 -27.3 0.788 -1.398\ncore.scoring.hbonds.HBondSet: #B 63 GLU N B 62 GLU OE2 2.31 142.0 107.1 -34.1 0.341 -0.378\ncore.scoring.hbonds.HBondSet: #B 68 ARG N B 64 TYR O 2.21 159.0 142.6 -170.1 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #B 66 ALA N B 68 ARG O 2.47 136.1 106.6 33.2 1.000 -0.418\ncore.scoring.hbonds.HBondSet: #B 69 ASP N B 67 MET O 1.74 106.9 117.0 -154.2 1.000 -0.195\ncore.scoring.hbonds.HBondSet: #B 70 GLN N B 67 MET O 1.98 119.6 120.4 -45.6 1.000 -0.524\ncore.scoring.hbonds.HBondSet: #B 71 TYR N B 67 MET O 2.16 162.9 149.0 67.5 1.000 -1.022\ncore.scoring.hbonds.HBondSet: #B 73 ARG N B 69 ASP O 2.51 126.5 117.9 -129.1 1.000 -0.007\ncore.scoring.hbonds.HBondSet: #B 73 ARG NH2B 69 ASP OD1 2.57 139.8 133.2 -39.3 0.459 -0.260\ncore.scoring.hbonds.HBondSet: #B 74 THR N B 70 GLN O 2.49 146.7 125.7 -106.1 1.000 -0.149\ncore.scoring.hbonds.HBondSet: #B 75 GLY N B 71 TYR O 1.87 145.5 145.5 -114.3 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #B 112 VAL N B 78 PHE O 2.16 146.2 176.3 179.0 1.000 -0.584\ncore.scoring.hbonds.HBondSet: #B 78 PHE N B 110 PRO O 2.04 158.2 134.9 -140.7 1.000 -1.502\ncore.scoring.hbonds.HBondSet: #B 114 VAL N B 80 CYS O 1.97 165.7 143.0 81.3 1.000 -1.057\ncore.scoring.hbonds.HBondSet: #B 80 CYS N B 112 VAL O 1.96 160.5 171.4 -82.6 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 116 ASN N B 82 PHE O 2.01 161.1 144.6 -120.6 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 86 ASN N B 83 ALA O 1.81 161.3 117.4 -107.2 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #B 83 ALA N B 89 SER OG 1.96 171.4 124.8 149.0 1.000 -2.326\ncore.scoring.hbonds.HBondSet: #B 84 ILE N B 116 ASN O 1.99 170.8 165.9 28.4 1.000 -1.215\ncore.scoring.hbonds.HBondSet: #B 124 THR N B 84 ILE O 2.25 143.4 147.0 -164.4 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 89 SER N B 86 ASN OD1 1.35 169.0 136.5 -89.4 0.929 -0.473\ncore.scoring.hbonds.HBondSet: #B 90 PHE N B 86 ASN O 2.39 149.6 128.9 -139.9 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 87 THR OG1B 124 THR OG1 1.94 120.7 134.4 95.7 0.576 -0.105\ncore.scoring.hbonds.HBondSet: #B 91 GLU N B 87 THR O 1.86 159.4 146.8 -126.5 1.000 -1.080\ncore.scoring.hbonds.HBondSet: #B 92 ASP N B 88 LYS O 2.02 132.2 148.3 -133.4 1.000 -0.579\ncore.scoring.hbonds.HBondSet: #B 96 TYR N B 92 ASP O 2.17 155.0 146.9 149.5 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #B 97 ARG N B 93 ILE O 2.00 161.9 151.3 -100.5 1.000 -1.005\ncore.scoring.hbonds.HBondSet: #B 98 GLU N B 94 HIS O 2.09 144.5 133.0 -121.8 1.000 -0.859\ncore.scoring.hbonds.HBondSet: #B 99 GLN N B 95 GLN O 1.75 174.2 171.9 -172.4 1.000 -0.848\ncore.scoring.hbonds.HBondSet: #B 100 ILE N B 96 TYR O 1.99 154.7 141.5 -129.9 1.000 -1.183\ncore.scoring.hbonds.HBondSet: #B 97 ARG NH1B 98 GLU OE1 2.08 102.1 136.3 167.3 0.600 -0.281\ncore.scoring.hbonds.HBondSet: #B 101 LYS N B 97 ARG O 2.20 169.3 146.3 -103.0 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 102 ARG N B 98 GLU O 2.10 155.0 157.1 -125.1 1.000 -0.944\ncore.scoring.hbonds.HBondSet: #B 103 VAL N B 99 GLN O 2.07 144.8 153.9 -148.4 1.000 -0.924\ncore.scoring.hbonds.HBondSet: #B 104 LYS N B 101 LYS O 2.32 156.3 98.4 -104.6 1.000 -0.333\ncore.scoring.hbonds.HBondSet: #B 105 ASP N B 101 LYS O 1.87 114.7 134.2 -113.9 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 106 SER N B 104 LYS O 2.12 146.8 90.6 135.1 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #B 142 ILE N B 113 LEU O 2.29 151.5 148.5 168.3 1.000 -1.122\ncore.scoring.hbonds.HBondSet: #B 113 LEU N B 140 PRO O 2.26 166.9 142.6 -106.9 1.000 -0.939\ncore.scoring.hbonds.HBondSet: #B 115 GLY N B 142 ILE O 1.89 175.4 163.3 115.9 1.000 -1.115\ncore.scoring.hbonds.HBondSet: #B 144 THR N B 115 GLY O 1.82 166.4 143.8 108.2 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #B 116 ASN ND2B 144 THR OG1 2.11 151.9 114.3 74.4 1.000 -1.625\ncore.scoring.hbonds.HBondSet: #B 120 LEU N B 117 LYS O 1.61 160.9 146.4 -148.9 1.000 -0.638\ncore.scoring.hbonds.HBondSet: #B 118 CYS N B 144 THR O 2.26 149.6 158.9 128.3 1.000 -0.664\ncore.scoring.hbonds.HBondSet: #B 122 ALA N B 120 LEU O 2.39 118.6 115.2 -135.1 1.000 -0.091\ncore.scoring.hbonds.HBondSet: #B 123 ARG NE B 125 VAL O 1.27 158.8 151.8 151.1 0.859 -0.468\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH1B 143 GLU OE1 2.43 152.6 131.2 154.5 0.835 -1.002\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH2B 143 GLU OE2 2.05 144.9 97.4 -150.9 0.835 -0.765\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 126 GLU O 2.05 144.5 148.6 -178.6 1.000 -1.206\ncore.scoring.hbonds.HBondSet: #B 126 GLU N B 129 GLN OE1 1.82 136.4 92.4 58.0 0.482 -0.121\ncore.scoring.hbonds.HBondSet: #B 129 GLN N B 126 GLU O 2.06 119.8 113.4 -80.2 1.000 -0.010\ncore.scoring.hbonds.HBondSet: #B 128 ARG NH2B 127 SER OG 1.74 118.8 110.7 98.3 0.435 -0.082\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 127 SER O 1.83 123.3 115.7 -86.8 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 131 GLN N B 127 SER O 1.62 168.0 152.9 134.3 1.000 -0.522\ncore.scoring.hbonds.HBondSet: #B 132 ASP N B 128 ARG O 1.71 157.8 144.0 -118.8 1.000 -0.662\ncore.scoring.hbonds.HBondSet: #B 133 LEU N B 129 GLN O 2.33 152.8 121.1 -102.2 1.000 -0.556\ncore.scoring.hbonds.HBondSet: #B 134 ALA N B 130 ALA O 1.84 166.9 159.5 -175.0 1.000 -1.226\ncore.scoring.hbonds.HBondSet: #B 135 ARG N B 131 GLN O 1.92 146.8 146.1 -91.4 1.000 -0.623\ncore.scoring.hbonds.HBondSet: #B 136 SER N B 132 ASP O 2.11 155.5 152.5 -172.9 1.000 -1.320\ncore.scoring.hbonds.HBondSet: #B 137 TYR N B 133 LEU O 2.17 133.9 144.9 -123.0 1.000 -0.463\ncore.scoring.hbonds.HBondSet: #B 138 GLY N B 134 ALA O 1.85 135.9 139.4 -133.7 1.000 -0.690\ncore.scoring.hbonds.HBondSet: #B 139 ILE N B 134 ALA O 1.78 172.1 146.2 58.4 1.000 -1.059\ncore.scoring.hbonds.HBondSet: #B 141 TYR OH B 143 GLU OE2 1.30 169.7 124.0 -22.7 0.953 -1.194\ncore.scoring.hbonds.HBondSet: #B 149 ARG N B 145 SER O 1.85 110.9 146.3 -130.1 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 148 THR N B 145 SER OG 2.10 165.0 108.1 -79.1 0.694 -2.084\ncore.scoring.hbonds.HBondSet: #B 145 SER N B 150 GLN O 1.80 163.2 158.2 -5.1 1.000 -1.148\ncore.scoring.hbonds.HBondSet: #B 150 GLN N B 148 THR OG1 2.31 163.9 114.4 48.9 0.576 -1.417\ncore.scoring.hbonds.HBondSet: #B 152 VAL N B 149 ARG O 2.57 162.8 114.6 -116.9 1.000 -0.414\ncore.scoring.hbonds.HBondSet: #B 155 ALA N B 151 GLY O 1.98 152.5 142.8 -118.1 1.000 -0.965\ncore.scoring.hbonds.HBondSet: #B 156 PHE N B 152 VAL O 2.52 168.0 149.9 -128.4 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #B 157 TYR N B 153 GLU O 2.01 159.5 148.4 -101.6 1.000 -0.968\ncore.scoring.hbonds.HBondSet: #B 158 THR N B 154 ASP O 1.96 151.7 136.5 -81.7 1.000 -0.789\ncore.scoring.hbonds.HBondSet: #B 159 LEU N B 155 ALA O 2.49 137.7 130.1 -132.6 1.000 -0.327\ncore.scoring.hbonds.HBondSet: #B 160 VAL N B 156 PHE O 2.28 136.6 138.3 -137.9 1.000 -0.671\ncore.scoring.hbonds.HBondSet: #B 161 ARG N B 157 TYR O 2.05 160.9 147.4 -145.4 1.000 -1.405\ncore.scoring.hbonds.HBondSet: #B 162 GLU N B 158 THR O 1.98 142.2 135.1 -129.6 1.000 -0.935\ncore.scoring.hbonds.HBondSet: #B 163 ILE N B 159 LEU O 2.27 145.9 130.6 -115.9 1.000 -0.628\ncore.scoring.hbonds.HBondSet: #B 164 ARG N B 160 VAL O 1.87 170.6 168.8 -122.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #B 165 GLN N B 161 ARG O 1.97 158.8 148.5 -96.5 1.000 -0.933\ncore.scoring.hbonds.HBondSet: #B 166 HIS N B 162 GLU O 2.15 141.4 126.0 -121.4 1.000 -0.756\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 163 ILE O 2.28 116.2 139.1 -144.3 1.000 -0.241\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 164 ARG O 2.22 148.2 99.2 -95.0 1.000 -0.254\ncore.scoring.hbonds.HBondSet: #B 168 LEU N B 165 GLN O 2.06 156.0 105.9 -96.2 1.000 -0.731\ncore.scoring.hbonds.HBondSet: #B 165 GLN NE2B 169 ARG O 2.02 154.2 163.2 -90.6 0.600 -0.731\ncore.scoring.hbonds.HBondSet: #C 2 THR N C 50 THR O 1.72 154.1 148.6 160.0 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 52 LEU N C 2 THR O 1.55 161.2 156.3 126.4 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #C 4 TYR OH C 49 GLU OE1 1.43 137.8 91.5 160.8 0.859 -0.322\ncore.scoring.hbonds.HBondSet: #C 4 TYR N C 52 LEU O 2.12 158.0 146.8 110.8 1.000 -0.956\ncore.scoring.hbonds.HBondSet: #C 54 ASP N C 4 TYR O 2.02 153.2 152.3 86.2 1.000 -0.814\ncore.scoring.hbonds.HBondSet: #C 5 LYS N C 76 GLU OE1 1.63 176.7 141.4 -69.2 0.718 -1.026\ncore.scoring.hbonds.HBondSet: #C 76 GLU N C 5 LYS O 1.69 153.2 142.2 -29.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #C 77 GLY N C 5 LYS O 2.17 159.7 146.5 136.1 1.000 -1.218\ncore.scoring.hbonds.HBondSet: #C 6 LEU N C 54 ASP O 2.32 137.6 138.1 85.2 1.000 -0.152\ncore.scoring.hbonds.HBondSet: #C 56 LEU N C 6 LEU O 1.75 173.5 163.1 -159.7 1.000 -0.981\ncore.scoring.hbonds.HBondSet: #C 7 VAL N C 77 GLY O 2.04 157.7 156.7 -176.3 1.000 -1.280\ncore.scoring.hbonds.HBondSet: #C 79 LEU N C 7 VAL O 2.04 161.1 151.4 106.5 1.000 -1.011\ncore.scoring.hbonds.HBondSet: #C 8 VAL N C 56 LEU O 1.70 168.1 175.5 -29.1 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #C 58 THR N C 8 VAL O 2.51 149.3 152.2 -34.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #C 81 VAL N C 9 VAL O 1.97 169.4 138.7 -95.1 1.000 -1.087\ncore.scoring.hbonds.HBondSet: #C 9 VAL N C 79 LEU O 1.99 163.0 158.5 69.8 1.000 -1.041\ncore.scoring.hbonds.HBondSet: #C 14 VAL N C 11 ALA O 2.53 152.2 138.8 -142.7 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #C 116 ASN ND2C 14 VAL O 1.82 167.4 146.4 -179.9 1.000 -1.537\ncore.scoring.hbonds.HBondSet: #C 20 THR N C 16 LYS O 1.99 167.4 144.5 -123.1 1.000 -1.282\ncore.scoring.hbonds.HBondSet: #C 21 ILE N C 17 SER O 1.82 165.5 158.8 -113.3 1.000 -0.929\ncore.scoring.hbonds.HBondSet: #C 22 GLN N C 18 ALA O 2.38 136.0 129.7 -113.7 1.000 -0.171\ncore.scoring.hbonds.HBondSet: #C 23 LEU N C 19 LEU O 2.36 161.8 147.0 -120.0 1.000 -0.796\ncore.scoring.hbonds.HBondSet: #C 24 ILE N C 20 THR O 2.00 166.6 151.1 -111.1 1.000 -1.125\ncore.scoring.hbonds.HBondSet: #C 25 GLN N C 21 ILE O 1.72 154.7 129.3 -67.1 1.000 -0.607\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 21 ILE O 2.57 119.1 135.6 -156.2 1.000 -0.015\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 22 GLN O 1.79 133.4 103.5 -60.3 1.000 -0.147\ncore.scoring.hbonds.HBondSet: #C 22 GLN NE2C 146 ALA O 1.63 154.0 167.5 -163.7 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #C 149 ARG NE C 22 GLN O 2.21 140.1 113.0 69.0 0.812 -0.272\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 22 GLN O 1.88 151.2 126.3 147.7 0.812 -1.210\ncore.scoring.hbonds.HBondSet: #C 42 LYS NZ C 23 LEU O 1.67 132.9 144.5 165.1 0.812 -0.372\ncore.scoring.hbonds.HBondSet: #C 27 HIS NE2C 25 GLN OE1 1.52 162.8 154.3 6.2 0.435 -1.662\ncore.scoring.hbonds.HBondSet: #C 38 ASP N C 57 ASP O 2.03 155.3 145.6 -28.1 1.000 -1.404\ncore.scoring.hbonds.HBondSet: #C 57 ASP N C 38 ASP O 1.79 175.4 159.9 -62.4 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #C 41 ARG NE C 40 TYR O 1.84 155.4 116.2 116.0 0.671 -0.817\ncore.scoring.hbonds.HBondSet: #C 40 TYR N C 55 ILE O 2.07 139.9 138.2 60.9 1.000 -0.682\ncore.scoring.hbonds.HBondSet: #C 55 ILE N C 40 TYR O 2.01 140.2 128.7 -92.3 1.000 -0.492\ncore.scoring.hbonds.HBondSet: #C 42 LYS N C 53 LEU O 1.92 154.7 134.6 29.2 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #C 53 LEU N C 42 LYS O 1.68 151.6 151.7 111.2 1.000 -0.308\ncore.scoring.hbonds.HBondSet: #C 44 VAL N C 51 CYS O 1.85 164.6 152.3 -11.9 1.000 -1.400\ncore.scoring.hbonds.HBondSet: #C 51 CYS N C 44 VAL O 1.80 154.4 157.7 -123.0 1.000 -0.742\ncore.scoring.hbonds.HBondSet: #C 46 ILE N C 49 GLU O 1.67 145.0 151.1 -29.9 1.000 -0.420\ncore.scoring.hbonds.HBondSet: #C 161 ARG NE C 47 ASP OD2 1.79 167.7 111.2 -154.9 0.741 -1.399\ncore.scoring.hbonds.HBondSet: #C 161 ARG NH2C 47 ASP OD1 1.31 152.2 114.3 134.3 0.741 -0.155\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH1C 47 ASP OD2 1.79 144.3 119.0 -34.0 0.694 -1.005\ncore.scoring.hbonds.HBondSet: #C 164 ARG NE C 49 GLU OE1 2.09 148.3 123.1 -106.5 0.765 -0.680\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH2C 49 GLU OE1 1.98 150.7 130.9 -21.0 0.765 -1.389\ncore.scoring.hbonds.HBondSet: #C 64 TYR N C 61 GLN O 2.09 163.3 134.6 -104.2 1.000 -1.046\ncore.scoring.hbonds.HBondSet: #C 67 MET N C 64 TYR O 2.24 163.1 120.2 -110.8 1.000 -0.992\ncore.scoring.hbonds.HBondSet: #C 68 ARG N C 65 SER O 2.45 162.1 114.3 -110.9 1.000 -0.588\ncore.scoring.hbonds.HBondSet: #C 71 TYR N C 67 MET O 2.78 160.9 130.8 -139.3 1.000 -0.124\ncore.scoring.hbonds.HBondSet: #C 72 MET N C 68 ARG O 1.90 156.3 161.6 -113.6 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 68 ARG NH1C 99 GLN OE1 2.34 152.0 138.5 126.6 0.718 -0.553\ncore.scoring.hbonds.HBondSet: #C 73 ARG N C 69 ASP O 2.24 126.8 126.8 -125.2 1.000 -0.354\ncore.scoring.hbonds.HBondSet: #C 74 THR N C 70 GLN O 2.31 145.5 139.3 -134.5 1.000 -0.795\ncore.scoring.hbonds.HBondSet: #C 75 GLY N C 71 TYR O 2.01 145.7 143.8 -113.0 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #C 78 PHE N C 110 PRO O 1.89 171.1 154.0 -133.0 1.000 -1.258\ncore.scoring.hbonds.HBondSet: #C 112 VAL N C 78 PHE O 2.26 137.9 153.6 -177.7 1.000 -0.706\ncore.scoring.hbonds.HBondSet: #C 114 VAL N C 80 CYS O 1.86 155.0 164.5 88.3 1.000 -0.760\ncore.scoring.hbonds.HBondSet: #C 80 CYS N C 112 VAL O 1.88 162.1 169.5 2.0 1.000 -1.001\ncore.scoring.hbonds.HBondSet: #C 82 PHE N C 114 VAL O 1.97 151.0 151.7 -114.5 1.000 -0.844\ncore.scoring.hbonds.HBondSet: #C 116 ASN N C 82 PHE O 1.73 153.8 170.9 -52.7 1.000 -0.479\ncore.scoring.hbonds.HBondSet: #C 86 ASN N C 83 ALA O 2.10 150.9 123.3 -107.8 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #C 83 ALA N C 89 SER OG 2.04 170.4 133.9 145.8 1.000 -2.012\ncore.scoring.hbonds.HBondSet: #C 84 ILE N C 116 ASN O 1.95 159.3 172.6 -73.4 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #C 124 THR N C 84 ILE O 1.76 153.0 166.8 -131.8 1.000 -0.587\ncore.scoring.hbonds.HBondSet: #C 125 VAL N C 84 ILE O 2.53 164.3 138.7 -65.9 1.000 -0.489\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN O 2.24 126.7 121.2 -94.4 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN OD1 2.15 151.2 132.2 -37.0 0.976 -1.308\ncore.scoring.hbonds.HBondSet: #C 90 PHE N C 86 ASN O 2.49 148.3 136.9 172.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #C 91 GLU N C 87 THR O 1.73 168.1 160.6 -136.9 1.000 -0.842\ncore.scoring.hbonds.HBondSet: #C 92 ASP N C 88 LYS O 1.77 142.1 145.1 -143.0 1.000 -0.721\ncore.scoring.hbonds.HBondSet: #C 93 ILE N C 89 SER O 2.27 134.8 151.0 -133.2 1.000 -0.401\ncore.scoring.hbonds.HBondSet: #C 95 GLN N C 92 ASP O 2.18 123.3 117.3 -80.6 1.000 -0.020\ncore.scoring.hbonds.HBondSet: #C 96 TYR N C 92 ASP O 2.15 160.9 154.3 168.7 1.000 -1.329\ncore.scoring.hbonds.HBondSet: #C 97 ARG N C 93 ILE O 1.67 175.6 168.1 -141.3 1.000 -0.605\ncore.scoring.hbonds.HBondSet: #C 98 GLU N C 94 HIS O 2.15 153.5 139.2 -126.1 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #C 99 GLN N C 95 GLN O 2.33 146.1 145.4 -117.0 1.000 -0.482\ncore.scoring.hbonds.HBondSet: #C 100 ILE N C 96 TYR O 2.09 167.1 158.5 -150.8 1.000 -1.289\ncore.scoring.hbonds.HBondSet: #C 101 LYS N C 97 ARG O 2.11 163.6 148.7 -126.8 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #C 102 ARG N C 98 GLU O 2.14 156.4 133.1 -120.4 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #C 103 VAL N C 99 GLN O 1.77 170.6 155.8 -107.8 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 104 LYS N C 100 ILE O 1.74 161.0 159.6 -109.4 1.000 -0.667\ncore.scoring.hbonds.HBondSet: #C 106 SER N C 101 LYS O 2.41 142.0 129.0 1.7 1.000 -1.169\ncore.scoring.hbonds.HBondSet: #C 102 ARG NH2C 105 ASP OD1 2.37 145.4 152.0 -158.6 0.318 -0.641\ncore.scoring.hbonds.HBondSet: #C 108 ASP N C 106 SER OG 2.22 135.0 142.4 -10.1 0.482 -0.020\ncore.scoring.hbonds.HBondSet: #C 169 ARG NH1C 108 ASP OD2 1.70 129.9 173.3 -0.5 0.412 -0.001\ncore.scoring.hbonds.HBondSet: #C 142 ILE N C 113 LEU O 1.88 166.1 166.9 171.9 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #C 113 LEU N C 140 PRO O 1.93 164.7 144.6 -108.0 1.000 -1.073\ncore.scoring.hbonds.HBondSet: #C 115 GLY N C 142 ILE O 2.04 164.1 154.8 175.7 1.000 -1.446\ncore.scoring.hbonds.HBondSet: #C 144 THR N C 115 GLY O 2.02 173.4 137.2 103.8 1.000 -1.173\ncore.scoring.hbonds.HBondSet: #C 120 LEU N C 117 LYS O 1.80 177.0 133.7 -108.6 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #C 118 CYS N C 144 THR O 1.85 163.3 151.8 126.7 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH1C 143 GLU OE1 2.17 169.7 110.4 151.0 0.765 -1.461\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 143 GLU OE2 1.91 161.0 121.8 -138.6 0.765 -1.288\ncore.scoring.hbonds.HBondSet: #C 123 ARG NE C 125 VAL O 2.03 131.2 124.9 118.0 0.718 -0.374\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 125 VAL O 1.68 140.4 134.2 -140.9 0.718 -0.735\ncore.scoring.hbonds.HBondSet: #C 130 ALA N C 126 GLU O 2.53 165.6 156.0 -159.6 1.000 -0.707\ncore.scoring.hbonds.HBondSet: #C 131 GLN N C 127 SER O 1.87 164.3 151.0 -110.2 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #C 132 ASP N C 128 ARG O 2.01 146.5 132.7 -107.0 1.000 -0.738\ncore.scoring.hbonds.HBondSet: #C 133 LEU N C 129 GLN O 1.98 143.1 129.4 -112.3 1.000 -0.717\ncore.scoring.hbonds.HBondSet: #C 134 ALA N C 130 ALA O 1.82 166.4 162.3 -156.9 1.000 -1.089\ncore.scoring.hbonds.HBondSet: #C 135 ARG N C 131 GLN O 2.10 173.9 148.9 -111.9 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #C 135 ARG NH1C 132 ASP OD1 2.38 136.5 145.6 -62.9 0.647 -0.181\ncore.scoring.hbonds.HBondSet: #C 136 SER N C 132 ASP O 2.12 152.8 137.7 -125.8 1.000 -1.072\ncore.scoring.hbonds.HBondSet: #C 137 TYR N C 133 LEU O 1.85 167.1 151.6 -134.6 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #C 139 ILE N C 134 ALA O 1.96 155.3 118.9 78.3 1.000 -0.895\ncore.scoring.hbonds.HBondSet: #C 141 TYR N D 43 GLN OE1 2.04 144.7 105.1 -161.4 0.882 -1.464\ncore.scoring.hbonds.HBondSet: #D 43 GLN NE2C 141 TYR O 2.03 157.6 130.4 65.6 0.882 -0.956\ncore.scoring.hbonds.HBondSet: #C 141 TYR OH C 143 GLU OE2 1.55 152.8 103.6 -1.4 0.929 -1.224\ncore.scoring.hbonds.HBondSet: #C 148 THR N C 145 SER OG 2.52 155.7 104.8 -76.2 0.718 -0.373\ncore.scoring.hbonds.HBondSet: #C 145 SER N C 150 GLN O 2.05 141.0 168.7 41.9 1.000 -0.559\ncore.scoring.hbonds.HBondSet: #C 152 VAL N C 149 ARG O 2.51 168.9 127.3 -107.7 1.000 -0.552\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH1C 153 GLU OE2 1.56 159.7 126.3 71.8 0.600 -0.384\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 153 GLU OE2 2.54 125.7 139.4 -17.5 0.600 -0.123\ncore.scoring.hbonds.HBondSet: #C 155 ALA N C 151 GLY O 1.78 146.1 133.1 -129.0 1.000 -0.800\ncore.scoring.hbonds.HBondSet: #C 156 PHE N C 152 VAL O 1.89 154.0 157.7 -140.7 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 157 TYR N C 153 GLU O 1.84 163.0 153.4 -86.5 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #C 158 THR N C 154 ASP O 1.94 154.1 142.2 -89.4 1.000 -0.813\ncore.scoring.hbonds.HBondSet: #C 159 LEU N C 155 ALA O 2.54 144.2 134.9 -128.1 1.000 -0.262\ncore.scoring.hbonds.HBondSet: #C 160 VAL N C 156 PHE O 2.21 149.1 137.4 -143.0 1.000 -1.172\ncore.scoring.hbonds.HBondSet: #C 161 ARG N C 157 TYR O 1.89 162.8 155.6 -160.3 1.000 -1.302\ncore.scoring.hbonds.HBondSet: #C 162 GLU N C 158 THR O 1.95 165.7 151.2 -131.2 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #C 163 ILE N C 159 LEU O 2.23 149.1 141.0 -119.3 1.000 -0.761\ncore.scoring.hbonds.HBondSet: #C 164 ARG N C 160 VAL O 1.88 171.9 160.2 -115.2 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 165 GLN N C 161 ARG O 1.82 176.3 172.4 -139.7 1.000 -0.999\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 162 GLU OE1 1.82 144.1 91.7 156.6 0.976 -0.691\ncore.scoring.hbonds.HBondSet: #C 166 HIS N C 162 GLU O 1.92 156.4 138.7 -120.0 1.000 -1.074\ncore.scoring.hbonds.HBondSet: #C 167 LYS N C 163 ILE O 2.12 124.3 130.8 -138.7 1.000 -0.641\ncore.scoring.hbonds.HBondSet: #C 168 LEU N C 164 ARG O 1.86 161.1 155.6 -106.6 1.000 -0.912\ncore.scoring.hbonds.HBondSet: #C 169 ARG N C 165 GLN O 2.29 139.6 150.6 -146.4 1.000 -0.622\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 165 GLN OE1 2.12 146.2 99.8 128.5 0.835 -0.554\ncore.scoring.hbonds.HBondSet: #C 171 LEU N C 168 LEU O 1.81 154.8 164.8 -70.6 1.000 -0.694\ncore.scoring.hbonds.HBondSet: #C 170 LYS NZ C 169 ARG O 1.86 133.9 108.9 117.0 0.224 -0.059\ncore.scoring.hbonds.HBondSet: #D 2 THR N D 50 THR O 1.98 153.0 167.9 155.1 1.000 -0.894\ncore.scoring.hbonds.HBondSet: #D 52 LEU N D 2 THR O 1.72 167.6 145.5 124.6 1.000 -0.897\ncore.scoring.hbonds.HBondSet: #D 4 TYR OH D 49 GLU OE1 1.87 148.2 90.6 -158.3 0.882 -0.520\ncore.scoring.hbonds.HBondSet: #D 4 TYR N D 52 LEU O 1.66 165.8 167.6 97.1 1.000 -0.435\ncore.scoring.hbonds.HBondSet: #D 54 ASP N D 4 TYR O 1.72 166.4 154.7 93.8 1.000 -0.648\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 4 TYR OH 2.59 162.8 134.0 74.5 0.882 -0.402\ncore.scoring.hbonds.HBondSet: #D 77 GLY N D 5 LYS O 2.52 134.7 154.4 -178.2 1.000 -0.113\ncore.scoring.hbonds.HBondSet: #D 5 LYS N D 76 GLU OE1 1.54 165.0 142.6 22.7 0.765 -1.391\ncore.scoring.hbonds.HBondSet: #D 76 GLU N D 5 LYS O 1.91 160.2 145.4 -56.2 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 56 LEU N D 6 LEU O 1.72 178.1 168.9 -117.8 1.000 -0.751\ncore.scoring.hbonds.HBondSet: #D 6 LEU N D 54 ASP O 1.90 160.8 152.3 94.5 1.000 -0.918\ncore.scoring.hbonds.HBondSet: #D 7 VAL N D 77 GLY O 2.11 157.8 159.9 -165.5 1.000 -1.145\ncore.scoring.hbonds.HBondSet: #D 79 LEU N D 7 VAL O 1.88 166.4 146.8 124.1 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #D 8 VAL N D 56 LEU O 1.77 169.6 175.1 81.8 1.000 -0.833\ncore.scoring.hbonds.HBondSet: #D 58 THR N D 8 VAL O 2.43 152.2 149.9 16.5 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #D 81 VAL N D 9 VAL O 1.75 169.0 165.2 144.8 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #D 9 VAL N D 79 LEU O 1.93 170.0 167.2 70.2 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #D 14 VAL N D 11 ALA O 2.38 148.7 141.4 -128.6 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #D 116 ASN ND2D 14 VAL O 1.67 147.0 135.1 141.6 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 19 LEU N D 15 GLY O 2.05 151.7 143.9 -99.6 1.000 -0.793\ncore.scoring.hbonds.HBondSet: #D 20 THR N D 16 LYS O 2.13 166.6 143.6 -107.4 1.000 -1.071\ncore.scoring.hbonds.HBondSet: #D 17 SER OG D 57 ASP OD2 1.87 114.6 107.7 -177.0 1.000 -0.488\ncore.scoring.hbonds.HBondSet: #D 21 ILE N D 17 SER O 1.79 154.9 149.8 -137.3 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 22 GLN N D 18 ALA O 1.86 153.5 140.6 -123.6 1.000 -0.977\ncore.scoring.hbonds.HBondSet: #D 23 LEU N D 19 LEU O 2.14 158.4 150.3 -145.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #D 24 ILE N D 20 THR O 2.07 155.1 140.7 -108.5 1.000 -0.925\ncore.scoring.hbonds.HBondSet: #D 25 GLN N D 21 ILE O 1.56 132.7 142.6 -9.3 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #D 26 ASN N D 21 ILE O 2.41 136.2 146.1 167.6 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #D 149 ARG NE D 22 GLN O 2.12 139.8 117.6 63.3 0.835 -0.464\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 22 GLN O 2.01 139.9 146.0 137.3 0.835 -0.652\ncore.scoring.hbonds.HBondSet: #D 29 VAL N D 27 HIS O 2.47 111.1 116.9 -152.8 1.000 -0.086\ncore.scoring.hbonds.HBondSet: #D 59 ALA N D 37 GLU OE1 2.23 169.0 99.2 -26.6 0.647 -0.979\ncore.scoring.hbonds.HBondSet: #D 57 ASP N D 38 ASP O 2.02 159.9 148.4 112.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 40 TYR N D 55 ILE O 1.66 150.7 149.5 -0.6 1.000 -0.730\ncore.scoring.hbonds.HBondSet: #D 55 ILE N D 40 TYR O 1.94 155.8 135.9 -80.6 1.000 -0.876\ncore.scoring.hbonds.HBondSet: #D 41 ARG NH2D 54 ASP OD1 2.11 156.8 122.7 133.7 0.647 -1.186\ncore.scoring.hbonds.HBondSet: #D 42 LYS N D 53 LEU O 2.24 133.2 129.7 31.0 1.000 -0.930\ncore.scoring.hbonds.HBondSet: #D 53 LEU N D 42 LYS O 1.82 169.1 144.4 75.9 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #D 42 LYS NZ D 157 TYR OH 2.05 139.6 157.2 168.5 0.812 -0.099\ncore.scoring.hbonds.HBondSet: #D 44 VAL N D 51 CYS O 1.90 142.6 139.5 2.6 1.000 -1.373\ncore.scoring.hbonds.HBondSet: #D 51 CYS N D 44 VAL O 1.71 161.1 161.3 18.3 1.000 -0.780\ncore.scoring.hbonds.HBondSet: #D 46 ILE N D 49 GLU O 1.90 136.6 145.3 -57.8 1.000 -0.553\ncore.scoring.hbonds.HBondSet: #D 49 GLU N D 46 ILE O 2.00 157.3 116.2 99.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 46 ILE O 2.07 136.9 109.4 -56.9 0.765 -0.451\ncore.scoring.hbonds.HBondSet: #D 161 ARG NE D 47 ASP OD2 1.82 167.5 111.8 -159.4 0.718 -1.487\ncore.scoring.hbonds.HBondSet: #D 161 ARG NH2D 47 ASP OD1 1.72 157.2 113.8 147.4 0.718 -1.127\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH1D 47 ASP OD2 2.23 122.1 98.1 -39.4 0.647 -0.042\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 49 GLU OE1 2.08 121.5 136.8 -92.4 0.765 -0.014\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 49 GLU OE1 1.40 140.1 138.2 49.8 0.765 -0.005\ncore.scoring.hbonds.HBondSet: #D 70 GLN N D 67 MET O 2.17 136.5 115.0 -98.6 1.000 -0.317\ncore.scoring.hbonds.HBondSet: #D 72 MET N D 68 ARG O 1.99 166.7 160.7 -170.5 1.000 -1.316\ncore.scoring.hbonds.HBondSet: #D 102 ARG NH1D 69 ASP OD2 2.19 136.9 124.8 139.4 0.459 -0.823\ncore.scoring.hbonds.HBondSet: #D 73 ARG N D 69 ASP O 1.97 140.8 139.1 -103.9 1.000 -0.550\ncore.scoring.hbonds.HBondSet: #D 74 THR N D 70 GLN O 2.16 137.2 131.6 -177.7 1.000 -1.376\ncore.scoring.hbonds.HBondSet: #D 75 GLY N D 72 MET O 2.38 158.1 105.7 -99.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #D 78 PHE N D 110 PRO O 2.05 157.7 144.7 -143.1 1.000 -1.368\ncore.scoring.hbonds.HBondSet: #D 112 VAL N D 78 PHE O 2.10 143.2 152.5 -172.7 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 114 VAL N D 80 CYS O 1.72 164.9 149.5 117.5 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 80 CYS N D 112 VAL O 1.95 161.0 172.9 34.9 1.000 -0.982\ncore.scoring.hbonds.HBondSet: #D 82 PHE N D 114 VAL O 2.03 167.4 170.3 75.0 1.000 -1.069\ncore.scoring.hbonds.HBondSet: #D 116 ASN N D 82 PHE O 2.12 146.4 173.7 -3.8 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #D 86 ASN N D 83 ALA O 2.54 144.5 114.1 -111.9 1.000 -0.035\ncore.scoring.hbonds.HBondSet: #D 83 ALA N D 89 SER OG 2.11 146.5 117.3 152.5 0.976 -1.646\ncore.scoring.hbonds.HBondSet: #D 124 THR N D 84 ILE O 1.93 160.3 139.9 136.2 1.000 -1.379\ncore.scoring.hbonds.HBondSet: #D 125 VAL N D 84 ILE O 2.05 139.0 162.4 -12.1 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #D 84 ILE N D 116 ASN O 1.94 147.6 177.3 -97.9 1.000 -0.661\ncore.scoring.hbonds.HBondSet: #D 89 SER N D 86 ASN OD1 2.00 161.6 108.1 -98.8 0.906 -0.997\ncore.scoring.hbonds.HBondSet: #D 90 PHE N D 86 ASN O 2.32 158.0 145.2 -158.1 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #D 91 GLU N D 87 THR O 1.78 158.6 144.7 -139.2 1.000 -1.110\ncore.scoring.hbonds.HBondSet: #D 88 LYS NZ D 91 GLU OE1 2.12 150.6 156.0 -89.7 0.459 -0.167\ncore.scoring.hbonds.HBondSet: #D 92 ASP N D 88 LYS O 1.73 149.1 145.6 -122.1 1.000 -0.547\ncore.scoring.hbonds.HBondSet: #D 93 ILE N D 90 PHE O 2.03 147.4 105.4 -96.7 1.000 -0.527\ncore.scoring.hbonds.HBondSet: #D 94 HIS N D 91 GLU O 2.28 154.2 119.5 -110.3 1.000 -0.747\ncore.scoring.hbonds.HBondSet: #D 95 GLN N D 92 ASP O 1.97 143.9 112.2 -97.6 1.000 -0.551\ncore.scoring.hbonds.HBondSet: #D 96 TYR N D 92 ASP O 2.30 161.1 156.2 175.1 1.000 -1.118\ncore.scoring.hbonds.HBondSet: #D 97 ARG N D 93 ILE O 2.05 176.1 164.5 -98.8 1.000 -1.133\ncore.scoring.hbonds.HBondSet: #D 98 GLU N D 94 HIS O 2.48 142.6 122.3 -120.3 1.000 -0.261\ncore.scoring.hbonds.HBondSet: #D 99 GLN N D 95 GLN O 1.99 161.3 153.0 -125.4 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 100 ILE N D 96 TYR O 1.87 177.4 169.1 -152.0 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #D 101 LYS N D 97 ARG O 1.86 167.3 142.3 -115.0 1.000 -1.108\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 98 GLU O 2.22 125.0 130.7 -126.1 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 99 GLN O 2.09 133.2 99.1 -93.1 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #D 103 VAL N D 99 GLN O 1.88 169.2 172.6 -128.9 1.000 -1.037\ncore.scoring.hbonds.HBondSet: #D 104 LYS N D 100 ILE O 1.81 170.9 160.9 -48.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 106 SER N D 101 LYS O 2.55 140.0 125.9 -41.0 1.000 -0.377\ncore.scoring.hbonds.HBondSet: #D 108 ASP N D 106 SER OG 2.21 137.3 143.4 13.5 0.459 -0.092\ncore.scoring.hbonds.HBondSet: #D 142 ILE N D 113 LEU O 2.18 165.5 165.0 143.8 1.000 -1.054\ncore.scoring.hbonds.HBondSet: #D 113 LEU N D 140 PRO O 1.99 168.8 165.8 -121.5 1.000 -1.121\ncore.scoring.hbonds.HBondSet: #D 144 THR N D 115 GLY O 2.05 151.3 119.0 102.4 1.000 -0.815\ncore.scoring.hbonds.HBondSet: #D 115 GLY N D 142 ILE O 2.14 152.6 145.4 126.2 1.000 -0.985\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 116 ASN OD1 1.95 135.6 102.0 -56.4 1.000 -0.502\ncore.scoring.hbonds.HBondSet: #D 146 ALA N D 116 ASN OD1 2.50 148.1 139.3 174.2 1.000 -0.040\ncore.scoring.hbonds.HBondSet: #D 120 LEU N D 117 LYS O 1.73 153.1 140.1 -82.7 1.000 -0.460\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 144 THR O 2.23 116.8 127.4 -123.2 1.000 -0.076\ncore.scoring.hbonds.HBondSet: #D 118 CYS N D 144 THR O 1.88 157.5 150.5 118.9 1.000 -0.964\ncore.scoring.hbonds.HBondSet: #D 123 ARG NE D 125 VAL O 1.82 128.0 130.3 143.5 0.624 -0.648\ncore.scoring.hbonds.HBondSet: #D 130 ALA N D 126 GLU O 2.57 166.7 149.2 -153.7 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 128 ARG NH2D 127 SER OG 2.10 123.3 96.6 53.1 0.412 -0.055\ncore.scoring.hbonds.HBondSet: #D 131 GLN N D 127 SER O 1.81 150.8 149.5 -138.0 1.000 -0.911\ncore.scoring.hbonds.HBondSet: #D 132 ASP N D 128 ARG O 1.96 143.7 138.7 -118.4 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #D 133 LEU N D 129 GLN O 2.05 154.0 149.6 -123.9 1.000 -1.006\ncore.scoring.hbonds.HBondSet: #D 134 ALA N D 130 ALA O 2.04 172.6 153.4 -117.2 1.000 -1.210\ncore.scoring.hbonds.HBondSet: #D 135 ARG N D 131 GLN O 2.00 157.8 139.8 -105.8 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 136 SER N D 132 ASP O 1.90 143.1 135.1 -132.5 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 137 TYR N D 133 LEU O 1.93 138.5 144.3 -145.7 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 134 ALA O 2.06 114.7 140.4 -145.1 1.000 -0.403\ncore.scoring.hbonds.HBondSet: #D 139 ILE N D 134 ALA O 1.90 169.0 134.7 69.1 1.000 -1.158\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 135 ARG O 2.19 144.5 99.6 -80.6 1.000 -0.216\ncore.scoring.hbonds.HBondSet: #D 141 TYR OH D 143 GLU OE2 1.45 141.9 141.2 32.0 0.906 -0.834\ncore.scoring.hbonds.HBondSet: #D 148 THR N D 145 SER OG 2.21 162.4 109.0 -94.6 0.718 -1.869\ncore.scoring.hbonds.HBondSet: #D 145 SER N D 150 GLN O 2.05 157.8 160.0 -28.2 1.000 -1.124\ncore.scoring.hbonds.HBondSet: #D 149 ARG N D 145 SER O 2.27 108.0 131.2 -130.5 1.000 0.000\ncore.scoring.hbonds.HBondSet: #D 150 GLN N D 148 THR OG1 2.01 159.2 116.7 54.1 0.553 -1.978\ncore.scoring.hbonds.HBondSet: #D 152 VAL N D 149 ARG O 2.08 167.7 133.5 -113.0 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH1D 153 GLU OE2 1.72 139.9 116.1 110.6 0.624 -0.269\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 153 GLU OE2 2.14 128.3 171.8 -38.7 0.624 -0.141\ncore.scoring.hbonds.HBondSet: #D 155 ALA N D 151 GLY O 2.21 144.4 149.7 -122.7 1.000 -0.640\ncore.scoring.hbonds.HBondSet: #D 156 PHE N D 152 VAL O 2.49 164.9 140.1 -133.1 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #D 157 TYR N D 153 GLU O 1.61 176.4 168.7 -139.5 1.000 -0.343\ncore.scoring.hbonds.HBondSet: #D 159 LEU N D 155 ALA O 2.52 140.7 130.8 -124.7 1.000 -0.182\ncore.scoring.hbonds.HBondSet: #D 160 VAL N D 156 PHE O 2.09 159.7 161.6 -154.7 1.000 -1.128\ncore.scoring.hbonds.HBondSet: #D 161 ARG N D 157 TYR O 2.63 167.6 136.4 -88.2 1.000 -0.115\ncore.scoring.hbonds.HBondSet: #D 162 GLU N D 158 THR O 2.14 149.2 143.1 -142.7 1.000 -1.147\ncore.scoring.hbonds.HBondSet: #D 163 ILE N D 159 LEU O 1.94 160.5 153.2 -126.9 1.000 -1.117\ncore.scoring.hbonds.HBondSet: #D 164 ARG N D 160 VAL O 1.61 159.8 154.1 -143.4 1.000 -0.367\ncore.scoring.hbonds.HBondSet: #D 165 GLN N D 161 ARG O 1.72 164.1 141.9 -98.0 1.000 -0.642\ncore.scoring.hbonds.HBondSet: #D 166 HIS N D 162 GLU O 1.79 161.8 144.1 -107.5 1.000 -0.839\ncore.scoring.hbonds.HBondSet: #D 167 LYS N D 163 ILE O 1.99 160.5 154.2 -112.8 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 168 LEU N D 165 GLN O 2.12 141.5 110.2 -100.9 1.000 -0.446\ncore.scoring.hbonds.HBondSet: #D 169 ARG N D 166 HIS O 1.83 168.3 146.2 -120.5 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #D 170 LYS N D 167 LYS O 2.34 150.5 125.7 -124.0 1.000 -0.782\ncore.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 162 GLU OE1 1.87 152.3 115.2 157.1 1.000 -1.850\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 165 GLN OE1 1.59 159.1 136.2 147.7 0.859 -1.567\ncore.scoring.hbonds.HBondSet: #A 52 LEU N A 2 THR O 1.59 171.0 149.6 134.7 1.000 -0.439\ncore.scoring.hbonds.HBondSet: #A 2 THR N A 50 THR O 2.01 158.3 155.0 -175.7 1.000 -1.342\ncore.scoring.hbonds.HBondSet: #A 4 TYR N A 52 LEU O 1.71 146.0 157.4 151.1 1.000 -0.468\ncore.scoring.hbonds.HBondSet: #A 54 ASP N A 4 TYR O 1.72 151.1 150.2 49.0 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #A 5 LYS N A 76 GLU OE1 1.52 175.1 149.4 13.9 0.765 -1.324\ncore.scoring.hbonds.HBondSet: #A 76 GLU N A 5 LYS O 1.97 142.0 123.6 -73.8 1.000 -0.616\ncore.scoring.hbonds.HBondSet: #A 77 GLY N A 5 LYS O 2.16 141.0 146.4 -155.0 1.000 -0.989\ncore.scoring.hbonds.HBondSet: #A 6 LEU N A 54 ASP O 1.88 169.2 151.8 102.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #A 56 LEU N A 6 LEU O 2.05 163.6 163.5 167.1 1.000 -1.200\ncore.scoring.hbonds.HBondSet: #A 7 VAL N A 77 GLY O 1.65 159.9 148.6 -140.0 1.000 -0.669\ncore.scoring.hbonds.HBondSet: #A 8 VAL N A 56 LEU O 2.14 166.5 145.2 73.7 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 8 VAL O 2.66 140.8 137.3 32.0 1.000 -0.139\ncore.scoring.hbonds.HBondSet: #A 81 VAL N A 9 VAL O 1.76 166.8 144.1 -124.3 1.000 -0.996\ncore.scoring.hbonds.HBondSet: #A 9 VAL N A 79 LEU O 1.98 138.4 151.4 57.5 1.000 -0.592\ncore.scoring.hbonds.HBondSet: #A 14 VAL N A 11 ALA O 1.88 154.8 146.6 -154.7 1.000 -1.324\ncore.scoring.hbonds.HBondSet: #A 117 LYS NZ A 13 GLY O 2.09 158.9 168.0 43.3 0.929 -0.307\ncore.scoring.hbonds.HBondSet: #A 116 ASN ND2A 14 VAL O 2.17 167.3 134.9 147.9 1.000 -1.433\ncore.scoring.hbonds.HBondSet: #A 19 LEU N A 15 GLY O 1.86 152.2 155.7 -122.2 1.000 -0.811\ncore.scoring.hbonds.HBondSet: #A 20 THR N A 16 LYS O 1.90 177.7 161.6 -167.9 1.000 -1.327\ncore.scoring.hbonds.HBondSet: #A 21 ILE N A 17 SER O 1.81 151.9 161.2 83.6 1.000 -0.613\ncore.scoring.hbonds.HBondSet: #A 17 SER OG A 57 ASP OD2 1.82 126.8 115.0 -166.4 1.000 -0.827\ncore.scoring.hbonds.HBondSet: #A 22 GLN N A 18 ALA O 2.31 140.8 122.1 -104.6 1.000 -0.323\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 19 LEU O 2.28 137.6 137.1 -174.9 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 20 THR O 1.97 123.1 112.5 -78.8 1.000 -0.055\ncore.scoring.hbonds.HBondSet: #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979\ncore.scoring.hbonds.HBondSet: #A 25 GLN N A 21 ILE O 2.24 105.4 127.6 -17.1 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 22 GLN O 1.69 156.8 124.3 126.5 0.859 -0.895\ncore.scoring.hbonds.HBondSet: #A 30 ASP N A 31 GLU OE2 1.95 148.8 110.5 52.5 0.318 -1.124\ncore.scoring.hbonds.HBondSet: #A 57 ASP N A 38 ASP O 2.02 149.5 176.9 -58.1 1.000 -0.727\ncore.scoring.hbonds.HBondSet: #A 40 TYR N A 55 ILE O 2.06 133.0 125.1 62.1 1.000 -0.543\ncore.scoring.hbonds.HBondSet: #A 55 ILE N A 40 TYR O 1.69 157.5 167.5 -58.5 1.000 -0.451\ncore.scoring.hbonds.HBondSet: #A 42 LYS N A 53 LEU O 2.02 144.4 129.4 31.9 1.000 -1.371\ncore.scoring.hbonds.HBondSet: #A 53 LEU N A 42 LYS O 1.74 153.8 165.7 -34.7 1.000 -0.598\ncore.scoring.hbonds.HBondSet: #A 43 GLN NE2B 141 TYR O 1.70 166.6 150.3 33.2 0.859 -1.175\ncore.scoring.hbonds.HBondSet: #B 141 TYR N A 43 GLN OE1 2.24 131.2 99.3 -167.7 0.859 -0.219\ncore.scoring.hbonds.HBondSet: #A 44 VAL N A 51 CYS O 1.71 163.4 149.6 -1.3 1.000 -1.165\ncore.scoring.hbonds.HBondSet: #A 46 ILE N A 49 GLU O 2.07 141.6 134.8 -34.7 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #A 49 GLU N A 46 ILE O 2.22 146.3 99.6 95.0 1.000 -0.222\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD1 2.30 127.4 91.6 172.3 0.718 -0.063\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD2 2.37 163.9 86.4 -172.5 0.718 -0.412\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH1A 47 ASP OD2 1.48 142.3 122.9 -33.8 0.671 -0.468\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH2A 47 ASP OD2 1.87 128.8 120.1 73.7 0.671 -0.154\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH1A 49 GLU OE2 1.85 136.1 126.0 132.0 0.624 -0.645\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH2A 49 GLU OE2 2.28 126.2 161.1 -104.1 0.624 -0.007\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 56 LEU O 2.50 117.5 111.9 -148.7 1.000 -0.051\ncore.scoring.hbonds.HBondSet: #A 65 SER N A 63 GLU OE1 1.63 154.5 118.5 115.9 0.224 -0.884\ncore.scoring.hbonds.HBondSet: #A 68 ARG NH2A 96 TYR OH 1.81 164.5 113.9 -150.2 0.788 -1.692\ncore.scoring.hbonds.HBondSet: #A 74 THR OG1A 71 TYR O 2.00 159.3 114.5 -39.3 0.576 -0.378\ncore.scoring.hbonds.HBondSet: #A 71 TYR N A 72 MET O 2.18 108.7 111.7 7.3 1.000 -0.617\ncore.scoring.hbonds.HBondSet: #A 75 GLY N A 71 TYR O 1.64 137.5 150.1 -159.0 1.000 -0.191\ncore.scoring.hbonds.HBondSet: #A 104 LYS NZ A 75 GLY O 1.73 151.1 175.2 27.0 0.788 -0.427\ncore.scoring.hbonds.HBondSet: #A 112 VAL N A 78 PHE O 2.25 148.8 157.4 173.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 78 PHE N A 110 PRO O 2.01 158.7 153.2 -144.4 1.000 -1.242\ncore.scoring.hbonds.HBondSet: #A 80 CYS N A 112 VAL O 2.27 143.1 149.0 68.7 1.000 -0.434\ncore.scoring.hbonds.HBondSet: #A 114 VAL N A 80 CYS O 2.23 169.9 156.5 101.6 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 116 ASN N A 82 PHE O 1.76 152.5 166.5 -98.5 1.000 -0.518\ncore.scoring.hbonds.HBondSet: #A 82 PHE N A 114 VAL O 2.14 145.0 155.1 -96.1 1.000 -0.561\ncore.scoring.hbonds.HBondSet: #A 86 ASN N A 83 ALA O 2.32 149.5 107.5 -109.9 1.000 -0.454\ncore.scoring.hbonds.HBondSet: #A 83 ALA N A 89 SER OG 1.92 159.9 113.0 146.0 1.000 -2.159\ncore.scoring.hbonds.HBondSet: #A 84 ILE N A 116 ASN O 2.25 158.9 161.3 -45.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 124 THR N A 84 ILE O 1.65 177.5 159.1 166.1 1.000 -0.788\ncore.scoring.hbonds.HBondSet: #A 88 LYS N A 86 ASN OD1 1.96 146.5 130.0 -97.6 0.600 -0.800\ncore.scoring.hbonds.HBondSet: #A 90 PHE N A 86 ASN O 2.39 155.4 153.6 -141.6 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #A 91 GLU N A 87 THR O 2.43 136.5 134.7 -143.4 1.000 -0.557\ncore.scoring.hbonds.HBondSet: #A 92 ASP N A 88 LYS O 2.28 145.5 141.1 -118.0 1.000 -0.589\ncore.scoring.hbonds.HBondSet: #A 96 TYR N A 92 ASP O 2.47 148.2 144.3 139.2 1.000 -0.571\ncore.scoring.hbonds.HBondSet: #A 95 GLN N A 92 ASP O 1.65 147.8 124.5 -102.5 1.000 -0.067\ncore.scoring.hbonds.HBondSet: #A 97 ARG N A 93 ILE O 2.13 156.0 164.2 -73.0 1.000 -0.838\ncore.scoring.hbonds.HBondSet: #A 98 GLU N A 94 HIS O 2.17 155.1 127.3 -111.1 1.000 -0.919\ncore.scoring.hbonds.HBondSet: #A 99 GLN N A 95 GLN O 2.20 147.3 151.5 -140.0 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #A 100 ILE N A 96 TYR O 2.07 160.1 159.6 177.7 1.000 -1.238\ncore.scoring.hbonds.HBondSet: #A 101 LYS N A 97 ARG O 2.17 173.1 164.2 -178.2 1.000 -1.217\ncore.scoring.hbonds.HBondSet: #A 102 ARG N A 98 GLU O 2.38 139.0 138.2 -136.4 1.000 -0.549\ncore.scoring.hbonds.HBondSet: #A 103 VAL N A 99 GLN O 1.71 166.8 162.3 -144.5 1.000 -0.762\ncore.scoring.hbonds.HBondSet: #A 104 LYS N A 100 ILE O 1.67 160.9 170.6 -154.6 1.000 -0.436\ncore.scoring.hbonds.HBondSet: #A 105 ASP N A 102 ARG O 2.25 143.4 93.6 -86.8 1.000 -0.002\ncore.scoring.hbonds.HBondSet: #A 108 ASP N A 106 SER OG 1.97 152.0 90.6 86.3 0.365 -1.113\ncore.scoring.hbonds.HBondSet: #A 113 LEU N A 140 PRO O 1.81 148.3 171.8 67.9 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #A 142 ILE N A 113 LEU O 1.79 150.9 160.0 151.3 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #A 115 GLY N A 142 ILE O 2.24 157.4 135.9 129.0 1.000 -1.120\ncore.scoring.hbonds.HBondSet: #A 144 THR N A 115 GLY O 2.13 162.0 119.4 101.2 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 116 ASN OD1 1.85 141.7 101.3 -66.8 1.000 -0.539\ncore.scoring.hbonds.HBondSet: #A 120 LEU N A 117 LYS O 1.95 172.9 143.4 -107.1 1.000 -1.171\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 144 THR O 2.01 106.8 129.9 -132.7 1.000 -0.125\ncore.scoring.hbonds.HBondSet: #A 118 CYS N A 144 THR O 1.90 170.5 123.4 123.6 1.000 -1.398\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 143 GLU OE2 1.95 158.1 107.0 -145.0 0.741 -1.215\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH2A 143 GLU OE1 1.63 171.8 119.9 158.6 0.741 -1.303\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 125 VAL O 2.02 173.1 148.1 -124.0 0.694 -1.007\ncore.scoring.hbonds.HBondSet: #A 130 ALA N A 126 GLU O 1.87 158.8 152.0 -177.9 1.000 -1.364\ncore.scoring.hbonds.HBondSet: #A 132 ASP N A 128 ARG O 2.21 150.7 138.4 -109.6 1.000 -0.724\ncore.scoring.hbonds.HBondSet: #A 133 LEU N A 129 GLN O 2.28 151.1 146.3 -142.0 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 134 ALA N A 130 ALA O 1.79 166.2 162.7 -178.5 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #A 135 ARG N A 131 GLN O 1.83 166.3 155.5 -99.9 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #A 136 SER N A 132 ASP O 1.78 156.7 145.2 -115.7 1.000 -0.779\ncore.scoring.hbonds.HBondSet: #A 137 TYR N A 133 LEU O 1.92 158.6 154.8 -155.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #A 138 GLY N A 134 ALA O 1.83 121.8 139.0 -163.6 1.000 -0.700\ncore.scoring.hbonds.HBondSet: #A 139 ILE N A 134 ALA O 2.24 163.7 126.8 83.5 1.000 -0.871\ncore.scoring.hbonds.HBondSet: #A 141 TYR OH A 143 GLU OE2 1.54 139.3 111.7 0.2 0.953 -1.165\ncore.scoring.hbonds.HBondSet: #A 141 TYR N C 43 GLN OE1 2.08 161.9 118.7 -172.1 0.835 -2.242\ncore.scoring.hbonds.HBondSet: #C 43 GLN NE2A 141 TYR O 2.33 146.4 124.9 79.1 0.835 -0.190\ncore.scoring.hbonds.HBondSet: #A 148 THR N A 145 SER OG 2.05 157.6 137.3 -91.6 0.694 -1.629\ncore.scoring.hbonds.HBondSet: #A 145 SER N A 150 GLN O 2.02 170.9 150.4 -53.6 1.000 -1.299\ncore.scoring.hbonds.HBondSet: #A 150 GLN N A 148 THR OG1 2.60 158.2 106.0 37.4 0.553 -0.009\ncore.scoring.hbonds.HBondSet: #A 152 VAL N A 149 ARG O 2.41 170.1 119.9 -103.6 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 153 GLU OE2 2.57 140.9 135.9 23.0 0.671 -0.460\ncore.scoring.hbonds.HBondSet: #A 155 ALA N A 151 GLY O 2.17 152.2 149.8 -130.5 1.000 -0.948\ncore.scoring.hbonds.HBondSet: #A 156 PHE N A 152 VAL O 2.47 167.0 144.2 -123.9 1.000 -0.728\ncore.scoring.hbonds.HBondSet: #A 157 TYR N A 153 GLU O 1.72 169.3 166.5 -179.4 1.000 -0.834\ncore.scoring.hbonds.HBondSet: #A 157 TYR OH A 153 GLU OE1 2.17 146.9 99.0 117.3 0.765 -0.012\ncore.scoring.hbonds.HBondSet: #A 158 THR N A 154 ASP O 1.89 147.3 139.5 -98.2 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #A 159 LEU N A 155 ALA O 2.17 148.5 137.9 -132.2 1.000 -1.027\ncore.scoring.hbonds.HBondSet: #A 160 VAL N A 156 PHE O 2.05 159.9 143.0 -132.0 1.000 -1.295\ncore.scoring.hbonds.HBondSet: #A 161 ARG N A 157 TYR O 1.81 160.4 153.3 -118.9 1.000 -0.892\ncore.scoring.hbonds.HBondSet: #A 162 GLU N A 158 THR O 2.08 152.2 148.4 -125.7 1.000 -0.984\ncore.scoring.hbonds.HBondSet: #A 163 ILE N A 159 LEU O 2.04 159.2 154.3 -135.6 1.000 -1.160\ncore.scoring.hbonds.HBondSet: #A 164 ARG N A 160 VAL O 1.82 170.5 164.7 -100.1 1.000 -0.943\ncore.scoring.hbonds.HBondSet: #A 165 GLN N A 161 ARG O 1.77 162.3 145.7 -126.0 1.000 -0.962\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 162 GLU OE2 1.52 173.9 111.2 -150.8 0.859 -1.532\ncore.scoring.hbonds.HBondSet: #A 166 HIS N A 162 GLU O 1.67 153.5 143.8 -117.4 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #A 167 LYS N A 163 ILE O 1.81 160.2 169.3 -164.8 1.000 -0.852\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 165 GLN OE1 1.68 168.3 116.6 -140.8 0.694 -1.841\ncore.scoring.hbonds.HBondSet: #A 168 LEU N A 165 GLN O 2.16 161.1 119.3 -109.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 167 LYS O 2.09 119.4 111.3 -127.2 1.000 -0.278\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 171 LEU O 2.31 134.6 103.8 72.2 1.000 -0.014\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 162 GLU OE2 1.78 162.3 101.4 -153.1 0.953 -1.514\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 165 GLN OE1 2.24 168.6 123.5 -111.6 0.741 -0.769\ncore.scoring.hbonds.HBondSet: #B 52 LEU N B 2 THR O 1.61 169.6 162.9 148.4 1.000 -0.412\ncore.scoring.hbonds.HBondSet: #B 2 THR N B 50 THR O 2.03 162.9 155.5 -160.6 1.000 -1.366\ncore.scoring.hbonds.HBondSet: #B 4 TYR N B 52 LEU O 1.80 164.8 167.3 95.8 1.000 -0.828\ncore.scoring.hbonds.HBondSet: #B 54 ASP N B 4 TYR O 1.94 154.4 155.9 57.8 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #B 4 TYR OH B 49 GLU OE1 1.84 151.6 105.5 143.8 0.812 -0.974\ncore.scoring.hbonds.HBondSet: #B 5 LYS N B 76 GLU OE1 1.53 174.9 152.7 -34.8 0.765 -1.099\ncore.scoring.hbonds.HBondSet: #B 76 GLU N B 5 LYS O 1.69 161.1 146.8 -26.4 1.000 -1.018\ncore.scoring.hbonds.HBondSet: #B 77 GLY N B 5 LYS O 2.40 143.5 155.6 146.2 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #B 6 LEU N B 54 ASP O 2.00 144.1 139.4 96.3 1.000 -0.600\ncore.scoring.hbonds.HBondSet: #B 56 LEU N B 6 LEU O 1.66 162.8 157.9 174.1 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #B 79 LEU N B 7 VAL O 1.74 157.3 152.8 147.5 1.000 -0.891\ncore.scoring.hbonds.HBondSet: #B 7 VAL N B 77 GLY O 2.02 174.4 161.6 166.4 1.000 -1.357\ncore.scoring.hbonds.HBondSet: #B 58 THR N B 8 VAL O 2.72 146.2 149.3 -11.1 1.000 -0.011\ncore.scoring.hbonds.HBondSet: #B 8 VAL N B 56 LEU O 1.97 177.7 162.1 69.5 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 9 VAL N B 79 LEU O 1.99 152.6 143.2 57.5 1.000 -1.020\ncore.scoring.hbonds.HBondSet: #B 81 VAL N B 9 VAL O 1.91 177.5 153.5 -123.6 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #B 14 VAL N B 11 ALA O 2.39 160.5 137.3 -127.2 1.000 -0.898\ncore.scoring.hbonds.HBondSet: #B 19 LEU N B 15 GLY O 1.91 147.7 148.4 -139.0 1.000 -0.998\ncore.scoring.hbonds.HBondSet: #B 20 THR N B 16 LYS O 1.82 178.0 165.1 -147.9 1.000 -1.102\ncore.scoring.hbonds.HBondSet: #B 21 ILE N B 17 SER O 1.94 143.6 134.8 -118.0 1.000 -0.775\ncore.scoring.hbonds.HBondSet: #B 17 SER OG B 57 ASP OD2 2.05 111.8 116.7 177.1 1.000 -0.366\ncore.scoring.hbonds.HBondSet: #B 22 GLN N B 18 ALA O 1.97 153.3 145.9 -100.8 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #B 23 LEU N B 19 LEU O 2.30 169.7 154.3 -159.7 1.000 -1.230\ncore.scoring.hbonds.HBondSet: #B 24 ILE N B 20 THR O 2.14 171.9 143.2 -132.6 1.000 -1.403\ncore.scoring.hbonds.HBondSet: #B 25 GLN N B 21 ILE O 1.99 147.2 133.1 -81.7 1.000 -0.687\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 21 ILE O 2.58 123.3 138.4 -158.7 1.000 -0.044\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 22 GLN O 1.79 133.6 118.3 -62.9 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #B 38 ASP N B 57 ASP O 1.85 160.4 146.8 -3.4 1.000 -1.515\ncore.scoring.hbonds.HBondSet: #B 57 ASP N B 38 ASP O 1.89 149.2 160.7 -105.2 1.000 -0.676\ncore.scoring.hbonds.HBondSet: #B 40 TYR N B 55 ILE O 2.11 143.2 150.5 52.1 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #B 55 ILE N B 40 TYR O 2.12 137.4 137.0 -91.8 1.000 -0.380\ncore.scoring.hbonds.HBondSet: #B 42 LYS N B 53 LEU O 1.91 134.3 138.2 49.9 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #B 44 VAL N B 51 CYS O 1.91 173.0 163.2 -19.0 1.000 -1.262\ncore.scoring.hbonds.HBondSet: #B 51 CYS N B 44 VAL O 1.70 159.6 163.0 112.3 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #B 46 ILE N B 49 GLU O 1.89 149.1 141.5 15.9 1.000 -1.413\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 46 ILE O 1.91 143.8 123.3 -75.0 0.835 -0.513\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD2 2.06 128.7 100.1 -167.7 0.718 -0.614\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD1 1.97 118.9 114.3 145.6 0.718 -0.498\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH1B 47 ASP OD2 1.52 144.2 128.2 -31.0 0.741 -0.595\ncore.scoring.hbonds.HBondSet: #B 164 ARG NE B 49 GLU OE1 2.22 142.9 142.9 -117.5 0.788 -0.542\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 49 GLU OE1 2.04 151.6 123.3 -27.3 0.788 -1.398\ncore.scoring.hbonds.HBondSet: #B 63 GLU N B 62 GLU OE2 2.31 142.0 107.1 -34.1 0.341 -0.378\ncore.scoring.hbonds.HBondSet: #B 68 ARG N B 64 TYR O 2.21 159.0 142.6 -170.1 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #B 66 ALA N B 68 ARG O 2.47 136.1 106.6 33.2 1.000 -0.418\ncore.scoring.hbonds.HBondSet: #B 69 ASP N B 67 MET O 1.74 106.9 117.0 -154.2 1.000 -0.195\ncore.scoring.hbonds.HBondSet: #B 70 GLN N B 67 MET O 1.98 119.6 120.4 -45.6 1.000 -0.524\ncore.scoring.hbonds.HBondSet: #B 71 TYR N B 67 MET O 2.16 162.9 149.0 67.5 1.000 -1.022\ncore.scoring.hbonds.HBondSet: #B 73 ARG N B 69 ASP O 2.51 126.5 117.9 -129.1 1.000 -0.007\ncore.scoring.hbonds.HBondSet: #B 73 ARG NH2B 69 ASP OD1 2.57 139.8 133.2 -39.3 0.459 -0.260\ncore.scoring.hbonds.HBondSet: #B 74 THR N B 70 GLN O 2.49 146.7 125.7 -106.1 1.000 -0.149\ncore.scoring.hbonds.HBondSet: #B 75 GLY N B 71 TYR O 1.87 145.5 145.5 -114.3 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #B 112 VAL N B 78 PHE O 2.16 146.2 176.3 179.0 1.000 -0.584\ncore.scoring.hbonds.HBondSet: #B 78 PHE N B 110 PRO O 2.04 158.2 134.9 -140.7 1.000 -1.502\ncore.scoring.hbonds.HBondSet: #B 114 VAL N B 80 CYS O 1.97 165.7 143.0 81.3 1.000 -1.057\ncore.scoring.hbonds.HBondSet: #B 80 CYS N B 112 VAL O 1.96 160.5 171.4 -82.6 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 116 ASN N B 82 PHE O 2.01 161.1 144.6 -120.6 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 86 ASN N B 83 ALA O 1.81 161.3 117.4 -107.2 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #B 83 ALA N B 89 SER OG 1.96 171.4 124.8 149.0 1.000 -2.326\ncore.scoring.hbonds.HBondSet: #B 84 ILE N B 116 ASN O 1.99 170.8 165.9 28.4 1.000 -1.215\ncore.scoring.hbonds.HBondSet: #B 124 THR N B 84 ILE O 2.25 143.4 147.0 -164.4 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 89 SER N B 86 ASN OD1 1.35 169.0 136.5 -89.4 0.929 -0.473\ncore.scoring.hbonds.HBondSet: #B 90 PHE N B 86 ASN O 2.39 149.6 128.9 -139.9 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 87 THR OG1B 124 THR OG1 1.94 120.7 134.4 95.7 0.576 -0.105\ncore.scoring.hbonds.HBondSet: #B 91 GLU N B 87 THR O 1.86 159.4 146.8 -126.5 1.000 -1.080\ncore.scoring.hbonds.HBondSet: #B 92 ASP N B 88 LYS O 2.02 132.2 148.3 -133.4 1.000 -0.579\ncore.scoring.hbonds.HBondSet: #B 96 TYR N B 92 ASP O 2.17 155.0 146.9 149.5 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #B 97 ARG N B 93 ILE O 2.00 161.9 151.3 -100.5 1.000 -1.005\ncore.scoring.hbonds.HBondSet: #B 98 GLU N B 94 HIS O 2.09 144.5 133.0 -121.8 1.000 -0.859\ncore.scoring.hbonds.HBondSet: #B 99 GLN N B 95 GLN O 1.75 174.2 171.9 -172.4 1.000 -0.848\ncore.scoring.hbonds.HBondSet: #B 100 ILE N B 96 TYR O 1.99 154.7 141.5 -129.9 1.000 -1.183\ncore.scoring.hbonds.HBondSet: #B 97 ARG NH1B 98 GLU OE1 2.08 102.1 136.3 167.3 0.600 -0.281\ncore.scoring.hbonds.HBondSet: #B 101 LYS N B 97 ARG O 2.20 169.3 146.3 -103.0 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 102 ARG N B 98 GLU O 2.10 155.0 157.1 -125.1 1.000 -0.944\ncore.scoring.hbonds.HBondSet: #B 103 VAL N B 99 GLN O 2.07 144.8 153.9 -148.4 1.000 -0.924\ncore.scoring.hbonds.HBondSet: #B 104 LYS N B 101 LYS O 2.32 156.3 98.4 -104.6 1.000 -0.333\ncore.scoring.hbonds.HBondSet: #B 105 ASP N B 101 LYS O 1.87 114.7 134.2 -113.9 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 106 SER N B 104 LYS O 2.12 146.8 90.6 135.1 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #B 142 ILE N B 113 LEU O 2.29 151.5 148.5 168.3 1.000 -1.122\ncore.scoring.hbonds.HBondSet: #B 113 LEU N B 140 PRO O 2.26 166.9 142.6 -106.9 1.000 -0.939\ncore.scoring.hbonds.HBondSet: #B 115 GLY N B 142 ILE O 1.89 175.4 163.3 115.9 1.000 -1.115\ncore.scoring.hbonds.HBondSet: #B 144 THR N B 115 GLY O 1.82 166.4 143.8 108.2 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #B 116 ASN ND2B 144 THR OG1 2.11 151.9 114.3 74.4 1.000 -1.625\ncore.scoring.hbonds.HBondSet: #B 120 LEU N B 117 LYS O 1.61 160.9 146.4 -148.9 1.000 -0.638\ncore.scoring.hbonds.HBondSet: #B 118 CYS N B 144 THR O 2.26 149.6 158.9 128.3 1.000 -0.664\ncore.scoring.hbonds.HBondSet: #B 122 ALA N B 120 LEU O 2.39 118.6 115.2 -135.1 1.000 -0.091\ncore.scoring.hbonds.HBondSet: #B 123 ARG NE B 125 VAL O 1.27 158.8 151.8 151.1 0.859 -0.468\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH1B 143 GLU OE1 2.43 152.6 131.2 154.5 0.835 -1.002\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH2B 143 GLU OE2 2.05 144.9 97.4 -150.9 0.835 -0.765\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 126 GLU O 2.05 144.5 148.6 -178.6 1.000 -1.206\ncore.scoring.hbonds.HBondSet: #B 126 GLU N B 129 GLN OE1 1.82 136.4 92.4 58.0 0.482 -0.121\ncore.scoring.hbonds.HBondSet: #B 129 GLN N B 126 GLU O 2.06 119.8 113.4 -80.2 1.000 -0.010\ncore.scoring.hbonds.HBondSet: #B 128 ARG NH2B 127 SER OG 1.74 118.8 110.7 98.3 0.435 -0.082\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 127 SER O 1.83 123.3 115.7 -86.8 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 131 GLN N B 127 SER O 1.62 168.0 152.9 134.3 1.000 -0.522\ncore.scoring.hbonds.HBondSet: #B 132 ASP N B 128 ARG O 1.71 157.8 144.0 -118.8 1.000 -0.662\ncore.scoring.hbonds.HBondSet: #B 133 LEU N B 129 GLN O 2.33 152.8 121.1 -102.2 1.000 -0.556\ncore.scoring.hbonds.HBondSet: #B 134 ALA N B 130 ALA O 1.84 166.9 159.5 -175.0 1.000 -1.226\ncore.scoring.hbonds.HBondSet: #B 135 ARG N B 131 GLN O 1.92 146.8 146.1 -91.4 1.000 -0.623\ncore.scoring.hbonds.HBondSet: #B 136 SER N B 132 ASP O 2.11 155.5 152.5 -172.9 1.000 -1.320\ncore.scoring.hbonds.HBondSet: #B 137 TYR N B 133 LEU O 2.17 133.9 144.9 -123.0 1.000 -0.463\ncore.scoring.hbonds.HBondSet: #B 138 GLY N B 134 ALA O 1.85 135.9 139.4 -133.7 1.000 -0.690\ncore.scoring.hbonds.HBondSet: #B 139 ILE N B 134 ALA O 1.78 172.1 146.2 58.4 1.000 -1.059\ncore.scoring.hbonds.HBondSet: #B 141 TYR OH B 143 GLU OE2 1.30 169.7 124.0 -22.7 0.953 -1.194\ncore.scoring.hbonds.HBondSet: #B 149 ARG N B 145 SER O 1.85 110.9 146.3 -130.1 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 148 THR N B 145 SER OG 2.10 165.0 108.1 -79.1 0.694 -2.084\ncore.scoring.hbonds.HBondSet: #B 145 SER N B 150 GLN O 1.80 163.2 158.2 -5.1 1.000 -1.148\ncore.scoring.hbonds.HBondSet: #B 150 GLN N B 148 THR OG1 2.31 163.9 114.4 48.9 0.576 -1.417\ncore.scoring.hbonds.HBondSet: #B 152 VAL N B 149 ARG O 2.57 162.8 114.6 -116.9 1.000 -0.414\ncore.scoring.hbonds.HBondSet: #B 155 ALA N B 151 GLY O 1.98 152.5 142.8 -118.1 1.000 -0.965\ncore.scoring.hbonds.HBondSet: #B 156 PHE N B 152 VAL O 2.52 168.0 149.9 -128.4 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #B 157 TYR N B 153 GLU O 2.01 159.5 148.4 -101.6 1.000 -0.968\ncore.scoring.hbonds.HBondSet: #B 158 THR N B 154 ASP O 1.96 151.7 136.5 -81.7 1.000 -0.789\ncore.scoring.hbonds.HBondSet: #B 159 LEU N B 155 ALA O 2.49 137.7 130.1 -132.6 1.000 -0.327\ncore.scoring.hbonds.HBondSet: #B 160 VAL N B 156 PHE O 2.28 136.6 138.3 -137.9 1.000 -0.671\ncore.scoring.hbonds.HBondSet: #B 161 ARG N B 157 TYR O 2.05 160.9 147.4 -145.4 1.000 -1.405\ncore.scoring.hbonds.HBondSet: #B 162 GLU N B 158 THR O 1.98 142.2 135.1 -129.6 1.000 -0.935\ncore.scoring.hbonds.HBondSet: #B 163 ILE N B 159 LEU O 2.27 145.9 130.6 -115.9 1.000 -0.628\ncore.scoring.hbonds.HBondSet: #B 164 ARG N B 160 VAL O 1.87 170.6 168.8 -122.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #B 165 GLN N B 161 ARG O 1.97 158.8 148.5 -96.5 1.000 -0.933\ncore.scoring.hbonds.HBondSet: #B 166 HIS N B 162 GLU O 2.15 141.4 126.0 -121.4 1.000 -0.756\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 163 ILE O 2.28 116.2 139.1 -144.3 1.000 -0.241\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 164 ARG O 2.22 148.2 99.2 -95.0 1.000 -0.254\ncore.scoring.hbonds.HBondSet: #B 168 LEU N B 165 GLN O 2.06 156.0 105.9 -96.2 1.000 -0.731\ncore.scoring.hbonds.HBondSet: #B 165 GLN NE2B 169 ARG O 2.02 154.2 163.2 -90.6 0.600 -0.731\ncore.scoring.hbonds.HBondSet: #C 2 THR N C 50 THR O 1.72 154.1 148.6 160.0 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 52 LEU N C 2 THR O 1.55 161.2 156.3 126.4 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #C 4 TYR OH C 49 GLU OE1 1.43 137.8 91.5 160.8 0.859 -0.322\ncore.scoring.hbonds.HBondSet: #C 4 TYR N C 52 LEU O 2.12 158.0 146.8 110.8 1.000 -0.956\ncore.scoring.hbonds.HBondSet: #C 54 ASP N C 4 TYR O 2.02 153.2 152.3 86.2 1.000 -0.814\ncore.scoring.hbonds.HBondSet: #C 5 LYS N C 76 GLU OE1 1.63 176.7 141.4 -69.2 0.718 -1.026\ncore.scoring.hbonds.HBondSet: #C 76 GLU N C 5 LYS O 1.69 153.2 142.2 -29.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #C 77 GLY N C 5 LYS O 2.17 159.7 146.5 136.1 1.000 -1.218\ncore.scoring.hbonds.HBondSet: #C 6 LEU N C 54 ASP O 2.32 137.6 138.1 85.2 1.000 -0.152\ncore.scoring.hbonds.HBondSet: #C 56 LEU N C 6 LEU O 1.75 173.5 163.1 -159.7 1.000 -0.981\ncore.scoring.hbonds.HBondSet: #C 7 VAL N C 77 GLY O 2.04 157.7 156.7 -176.3 1.000 -1.280\ncore.scoring.hbonds.HBondSet: #C 79 LEU N C 7 VAL O 2.04 161.1 151.4 106.5 1.000 -1.011\ncore.scoring.hbonds.HBondSet: #C 8 VAL N C 56 LEU O 1.70 168.1 175.5 -29.1 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #C 58 THR N C 8 VAL O 2.51 149.3 152.2 -34.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #C 81 VAL N C 9 VAL O 1.97 169.4 138.7 -95.1 1.000 -1.087\ncore.scoring.hbonds.HBondSet: #C 9 VAL N C 79 LEU O 1.99 163.0 158.5 69.8 1.000 -1.041\ncore.scoring.hbonds.HBondSet: #C 14 VAL N C 11 ALA O 2.53 152.2 138.8 -142.7 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #C 116 ASN ND2C 14 VAL O 1.82 167.4 146.4 -179.9 1.000 -1.537\ncore.scoring.hbonds.HBondSet: #C 20 THR N C 16 LYS O 1.99 167.4 144.5 -123.1 1.000 -1.282\ncore.scoring.hbonds.HBondSet: #C 21 ILE N C 17 SER O 1.82 165.5 158.8 -113.3 1.000 -0.929\ncore.scoring.hbonds.HBondSet: #C 22 GLN N C 18 ALA O 2.38 136.0 129.7 -113.7 1.000 -0.171\ncore.scoring.hbonds.HBondSet: #C 23 LEU N C 19 LEU O 2.36 161.8 147.0 -120.0 1.000 -0.796\ncore.scoring.hbonds.HBondSet: #C 24 ILE N C 20 THR O 2.00 166.6 151.1 -111.1 1.000 -1.125\ncore.scoring.hbonds.HBondSet: #C 25 GLN N C 21 ILE O 1.72 154.7 129.3 -67.1 1.000 -0.607\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 21 ILE O 2.57 119.1 135.6 -156.2 1.000 -0.015\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 22 GLN O 1.79 133.4 103.5 -60.3 1.000 -0.147\ncore.scoring.hbonds.HBondSet: #C 22 GLN NE2C 146 ALA O 1.63 154.0 167.5 -163.7 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #C 149 ARG NE C 22 GLN O 2.21 140.1 113.0 69.0 0.812 -0.272\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 22 GLN O 1.88 151.2 126.3 147.7 0.812 -1.210\ncore.scoring.hbonds.HBondSet: #C 42 LYS NZ C 23 LEU O 1.67 132.9 144.5 165.1 0.812 -0.372\ncore.scoring.hbonds.HBondSet: #C 27 HIS NE2C 25 GLN OE1 1.52 162.8 154.3 6.2 0.435 -1.662\ncore.scoring.hbonds.HBondSet: #C 38 ASP N C 57 ASP O 2.03 155.3 145.6 -28.1 1.000 -1.404\ncore.scoring.hbonds.HBondSet: #C 57 ASP N C 38 ASP O 1.79 175.4 159.9 -62.4 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #C 41 ARG NE C 40 TYR O 1.84 155.4 116.2 116.0 0.671 -0.817\ncore.scoring.hbonds.HBondSet: #C 40 TYR N C 55 ILE O 2.07 139.9 138.2 60.9 1.000 -0.682\ncore.scoring.hbonds.HBondSet: #C 55 ILE N C 40 TYR O 2.01 140.2 128.7 -92.3 1.000 -0.492\ncore.scoring.hbonds.HBondSet: #C 42 LYS N C 53 LEU O 1.92 154.7 134.6 29.2 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #C 53 LEU N C 42 LYS O 1.68 151.6 151.7 111.2 1.000 -0.308\ncore.scoring.hbonds.HBondSet: #C 44 VAL N C 51 CYS O 1.85 164.6 152.3 -11.9 1.000 -1.400\ncore.scoring.hbonds.HBondSet: #C 51 CYS N C 44 VAL O 1.80 154.4 157.7 -123.0 1.000 -0.742\ncore.scoring.hbonds.HBondSet: #C 46 ILE N C 49 GLU O 1.67 145.0 151.1 -29.9 1.000 -0.420\ncore.scoring.hbonds.HBondSet: #C 161 ARG NE C 47 ASP OD2 1.79 167.7 111.2 -154.9 0.741 -1.399\ncore.scoring.hbonds.HBondSet: #C 161 ARG NH2C 47 ASP OD1 1.31 152.2 114.3 134.3 0.741 -0.155\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH1C 47 ASP OD2 1.79 144.3 119.0 -34.0 0.694 -1.005\ncore.scoring.hbonds.HBondSet: #C 164 ARG NE C 49 GLU OE1 2.09 148.3 123.1 -106.5 0.765 -0.680\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH2C 49 GLU OE1 1.98 150.7 130.9 -21.0 0.765 -1.389\ncore.scoring.hbonds.HBondSet: #C 64 TYR N C 61 GLN O 2.09 163.3 134.6 -104.2 1.000 -1.046\ncore.scoring.hbonds.HBondSet: #C 67 MET N C 64 TYR O 2.24 163.1 120.2 -110.8 1.000 -0.992\ncore.scoring.hbonds.HBondSet: #C 68 ARG N C 65 SER O 2.45 162.1 114.3 -110.9 1.000 -0.588\ncore.scoring.hbonds.HBondSet: #C 71 TYR N C 67 MET O 2.78 160.9 130.8 -139.3 1.000 -0.124\ncore.scoring.hbonds.HBondSet: #C 72 MET N C 68 ARG O 1.90 156.3 161.6 -113.6 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 68 ARG NH1C 99 GLN OE1 2.34 152.0 138.5 126.6 0.718 -0.553\ncore.scoring.hbonds.HBondSet: #C 73 ARG N C 69 ASP O 2.24 126.8 126.8 -125.2 1.000 -0.354\ncore.scoring.hbonds.HBondSet: #C 74 THR N C 70 GLN O 2.31 145.5 139.3 -134.5 1.000 -0.795\ncore.scoring.hbonds.HBondSet: #C 75 GLY N C 71 TYR O 2.01 145.7 143.8 -113.0 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #C 78 PHE N C 110 PRO O 1.89 171.1 154.0 -133.0 1.000 -1.258\ncore.scoring.hbonds.HBondSet: #C 112 VAL N C 78 PHE O 2.26 137.9 153.6 -177.7 1.000 -0.706\ncore.scoring.hbonds.HBondSet: #C 114 VAL N C 80 CYS O 1.86 155.0 164.5 88.3 1.000 -0.760\ncore.scoring.hbonds.HBondSet: #C 80 CYS N C 112 VAL O 1.88 162.1 169.5 2.0 1.000 -1.001\ncore.scoring.hbonds.HBondSet: #C 82 PHE N C 114 VAL O 1.97 151.0 151.7 -114.5 1.000 -0.844\ncore.scoring.hbonds.HBondSet: #C 116 ASN N C 82 PHE O 1.73 153.8 170.9 -52.7 1.000 -0.479\ncore.scoring.hbonds.HBondSet: #C 86 ASN N C 83 ALA O 2.10 150.9 123.3 -107.8 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #C 83 ALA N C 89 SER OG 2.04 170.4 133.9 145.8 1.000 -2.012\ncore.scoring.hbonds.HBondSet: #C 84 ILE N C 116 ASN O 1.95 159.3 172.6 -73.4 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #C 124 THR N C 84 ILE O 1.76 153.0 166.8 -131.8 1.000 -0.587\ncore.scoring.hbonds.HBondSet: #C 125 VAL N C 84 ILE O 2.53 164.3 138.7 -65.9 1.000 -0.489\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN O 2.24 126.7 121.2 -94.4 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN OD1 2.15 151.2 132.2 -37.0 0.976 -1.308\ncore.scoring.hbonds.HBondSet: #C 90 PHE N C 86 ASN O 2.49 148.3 136.9 172.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #C 91 GLU N C 87 THR O 1.73 168.1 160.6 -136.9 1.000 -0.842\ncore.scoring.hbonds.HBondSet: #C 92 ASP N C 88 LYS O 1.77 142.1 145.1 -143.0 1.000 -0.721\ncore.scoring.hbonds.HBondSet: #C 93 ILE N C 89 SER O 2.27 134.8 151.0 -133.2 1.000 -0.401\ncore.scoring.hbonds.HBondSet: #C 95 GLN N C 92 ASP O 2.18 123.3 117.3 -80.6 1.000 -0.020\ncore.scoring.hbonds.HBondSet: #C 96 TYR N C 92 ASP O 2.15 160.9 154.3 168.7 1.000 -1.329\ncore.scoring.hbonds.HBondSet: #C 97 ARG N C 93 ILE O 1.67 175.6 168.1 -141.3 1.000 -0.605\ncore.scoring.hbonds.HBondSet: #C 98 GLU N C 94 HIS O 2.15 153.5 139.2 -126.1 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #C 99 GLN N C 95 GLN O 2.33 146.1 145.4 -117.0 1.000 -0.482\ncore.scoring.hbonds.HBondSet: #C 100 ILE N C 96 TYR O 2.09 167.1 158.5 -150.8 1.000 -1.289\ncore.scoring.hbonds.HBondSet: #C 101 LYS N C 97 ARG O 2.11 163.6 148.7 -126.8 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #C 102 ARG N C 98 GLU O 2.14 156.4 133.1 -120.4 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #C 103 VAL N C 99 GLN O 1.77 170.6 155.8 -107.8 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 104 LYS N C 100 ILE O 1.74 161.0 159.6 -109.4 1.000 -0.667\ncore.scoring.hbonds.HBondSet: #C 106 SER N C 101 LYS O 2.41 142.0 129.0 1.7 1.000 -1.169\ncore.scoring.hbonds.HBondSet: #C 102 ARG NH2C 105 ASP OD1 2.37 145.4 152.0 -158.6 0.318 -0.641\ncore.scoring.hbonds.HBondSet: #C 108 ASP N C 106 SER OG 2.22 135.0 142.4 -10.1 0.482 -0.020\ncore.scoring.hbonds.HBondSet: #C 169 ARG NH1C 108 ASP OD2 1.70 129.9 173.3 -0.5 0.412 -0.001\ncore.scoring.hbonds.HBondSet: #C 142 ILE N C 113 LEU O 1.88 166.1 166.9 171.9 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #C 113 LEU N C 140 PRO O 1.93 164.7 144.6 -108.0 1.000 -1.073\ncore.scoring.hbonds.HBondSet: #C 115 GLY N C 142 ILE O 2.04 164.1 154.8 175.7 1.000 -1.446\ncore.scoring.hbonds.HBondSet: #C 144 THR N C 115 GLY O 2.02 173.4 137.2 103.8 1.000 -1.173\ncore.scoring.hbonds.HBondSet: #C 120 LEU N C 117 LYS O 1.80 177.0 133.7 -108.6 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #C 118 CYS N C 144 THR O 1.85 163.3 151.8 126.7 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH1C 143 GLU OE1 2.17 169.7 110.4 151.0 0.765 -1.461\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 143 GLU OE2 1.91 161.0 121.8 -138.6 0.765 -1.288\ncore.scoring.hbonds.HBondSet: #C 123 ARG NE C 125 VAL O 2.03 131.2 124.9 118.0 0.718 -0.374\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 125 VAL O 1.68 140.4 134.2 -140.9 0.718 -0.735\ncore.scoring.hbonds.HBondSet: #C 130 ALA N C 126 GLU O 2.53 165.6 156.0 -159.6 1.000 -0.707\ncore.scoring.hbonds.HBondSet: #C 131 GLN N C 127 SER O 1.87 164.3 151.0 -110.2 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #C 132 ASP N C 128 ARG O 2.01 146.5 132.7 -107.0 1.000 -0.738\ncore.scoring.hbonds.HBondSet: #C 133 LEU N C 129 GLN O 1.98 143.1 129.4 -112.3 1.000 -0.717\ncore.scoring.hbonds.HBondSet: #C 134 ALA N C 130 ALA O 1.82 166.4 162.3 -156.9 1.000 -1.089\ncore.scoring.hbonds.HBondSet: #C 135 ARG N C 131 GLN O 2.10 173.9 148.9 -111.9 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #C 135 ARG NH1C 132 ASP OD1 2.38 136.5 145.6 -62.9 0.647 -0.181\ncore.scoring.hbonds.HBondSet: #C 136 SER N C 132 ASP O 2.12 152.8 137.7 -125.8 1.000 -1.072\ncore.scoring.hbonds.HBondSet: #C 137 TYR N C 133 LEU O 1.85 167.1 151.6 -134.6 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #C 139 ILE N C 134 ALA O 1.96 155.3 118.9 78.3 1.000 -0.895\ncore.scoring.hbonds.HBondSet: #C 141 TYR N D 43 GLN OE1 2.04 144.7 105.1 -161.4 0.882 -1.464\ncore.scoring.hbonds.HBondSet: #D 43 GLN NE2C 141 TYR O 2.03 157.6 130.4 65.6 0.882 -0.956\ncore.scoring.hbonds.HBondSet: #C 141 TYR OH C 143 GLU OE2 1.55 152.8 103.6 -1.4 0.929 -1.224\ncore.scoring.hbonds.HBondSet: #C 148 THR N C 145 SER OG 2.52 155.7 104.8 -76.2 0.718 -0.373\ncore.scoring.hbonds.HBondSet: #C 145 SER N C 150 GLN O 2.05 141.0 168.7 41.9 1.000 -0.559\ncore.scoring.hbonds.HBondSet: #C 152 VAL N C 149 ARG O 2.51 168.9 127.3 -107.7 1.000 -0.552\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH1C 153 GLU OE2 1.56 159.7 126.3 71.8 0.600 -0.384\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 153 GLU OE2 2.54 125.7 139.4 -17.5 0.600 -0.123\ncore.scoring.hbonds.HBondSet: #C 155 ALA N C 151 GLY O 1.78 146.1 133.1 -129.0 1.000 -0.800\ncore.scoring.hbonds.HBondSet: #C 156 PHE N C 152 VAL O 1.89 154.0 157.7 -140.7 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 157 TYR N C 153 GLU O 1.84 163.0 153.4 -86.5 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #C 158 THR N C 154 ASP O 1.94 154.1 142.2 -89.4 1.000 -0.813\ncore.scoring.hbonds.HBondSet: #C 159 LEU N C 155 ALA O 2.54 144.2 134.9 -128.1 1.000 -0.262\ncore.scoring.hbonds.HBondSet: #C 160 VAL N C 156 PHE O 2.21 149.1 137.4 -143.0 1.000 -1.172\ncore.scoring.hbonds.HBondSet: #C 161 ARG N C 157 TYR O 1.89 162.8 155.6 -160.3 1.000 -1.302\ncore.scoring.hbonds.HBondSet: #C 162 GLU N C 158 THR O 1.95 165.7 151.2 -131.2 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #C 163 ILE N C 159 LEU O 2.23 149.1 141.0 -119.3 1.000 -0.761\ncore.scoring.hbonds.HBondSet: #C 164 ARG N C 160 VAL O 1.88 171.9 160.2 -115.2 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 165 GLN N C 161 ARG O 1.82 176.3 172.4 -139.7 1.000 -0.999\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 162 GLU OE1 1.82 144.1 91.7 156.6 0.976 -0.691\ncore.scoring.hbonds.HBondSet: #C 166 HIS N C 162 GLU O 1.92 156.4 138.7 -120.0 1.000 -1.074\ncore.scoring.hbonds.HBondSet: #C 167 LYS N C 163 ILE O 2.12 124.3 130.8 -138.7 1.000 -0.641\ncore.scoring.hbonds.HBondSet: #C 168 LEU N C 164 ARG O 1.86 161.1 155.6 -106.6 1.000 -0.912\ncore.scoring.hbonds.HBondSet: #C 169 ARG N C 165 GLN O 2.29 139.6 150.6 -146.4 1.000 -0.622\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 165 GLN OE1 2.12 146.2 99.8 128.5 0.835 -0.554\ncore.scoring.hbonds.HBondSet: #C 171 LEU N C 168 LEU O 1.81 154.8 164.8 -70.6 1.000 -0.694\ncore.scoring.hbonds.HBondSet: #C 170 LYS NZ C 169 ARG O 1.86 133.9 108.9 117.0 0.224 -0.059\ncore.scoring.hbonds.HBondSet: #D 2 THR N D 50 THR O 1.98 153.0 167.9 155.1 1.000 -0.894\ncore.scoring.hbonds.HBondSet: #D 52 LEU N D 2 THR O 1.72 167.6 145.5 124.6 1.000 -0.897\ncore.scoring.hbonds.HBondSet: #D 4 TYR OH D 49 GLU OE1 1.87 148.2 90.6 -158.3 0.882 -0.520\ncore.scoring.hbonds.HBondSet: #D 4 TYR N D 52 LEU O 1.66 165.8 167.6 97.1 1.000 -0.435\ncore.scoring.hbonds.HBondSet: #D 54 ASP N D 4 TYR O 1.72 166.4 154.7 93.8 1.000 -0.648\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 4 TYR OH 2.59 162.8 134.0 74.5 0.882 -0.402\ncore.scoring.hbonds.HBondSet: #D 77 GLY N D 5 LYS O 2.52 134.7 154.4 -178.2 1.000 -0.113\ncore.scoring.hbonds.HBondSet: #D 5 LYS N D 76 GLU OE1 1.54 165.0 142.6 22.7 0.765 -1.391\ncore.scoring.hbonds.HBondSet: #D 76 GLU N D 5 LYS O 1.91 160.2 145.4 -56.2 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 56 LEU N D 6 LEU O 1.72 178.1 168.9 -117.8 1.000 -0.751\ncore.scoring.hbonds.HBondSet: #D 6 LEU N D 54 ASP O 1.90 160.8 152.3 94.5 1.000 -0.918\ncore.scoring.hbonds.HBondSet: #D 7 VAL N D 77 GLY O 2.11 157.8 159.9 -165.5 1.000 -1.145\ncore.scoring.hbonds.HBondSet: #D 79 LEU N D 7 VAL O 1.88 166.4 146.8 124.1 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #D 8 VAL N D 56 LEU O 1.77 169.6 175.1 81.8 1.000 -0.833\ncore.scoring.hbonds.HBondSet: #D 58 THR N D 8 VAL O 2.43 152.2 149.9 16.5 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #D 81 VAL N D 9 VAL O 1.75 169.0 165.2 144.8 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #D 9 VAL N D 79 LEU O 1.93 170.0 167.2 70.2 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #D 14 VAL N D 11 ALA O 2.38 148.7 141.4 -128.6 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #D 116 ASN ND2D 14 VAL O 1.67 147.0 135.1 141.6 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 19 LEU N D 15 GLY O 2.05 151.7 143.9 -99.6 1.000 -0.793\ncore.scoring.hbonds.HBondSet: #D 20 THR N D 16 LYS O 2.13 166.6 143.6 -107.4 1.000 -1.071\ncore.scoring.hbonds.HBondSet: #D 17 SER OG D 57 ASP OD2 1.87 114.6 107.7 -177.0 1.000 -0.488\ncore.scoring.hbonds.HBondSet: #D 21 ILE N D 17 SER O 1.79 154.9 149.8 -137.3 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 22 GLN N D 18 ALA O 1.86 153.5 140.6 -123.6 1.000 -0.977\ncore.scoring.hbonds.HBondSet: #D 23 LEU N D 19 LEU O 2.14 158.4 150.3 -145.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #D 24 ILE N D 20 THR O 2.07 155.1 140.7 -108.5 1.000 -0.925\ncore.scoring.hbonds.HBondSet: #D 25 GLN N D 21 ILE O 1.56 132.7 142.6 -9.3 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #D 26 ASN N D 21 ILE O 2.41 136.2 146.1 167.6 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #D 149 ARG NE D 22 GLN O 2.12 139.8 117.6 63.3 0.835 -0.464\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 22 GLN O 2.01 139.9 146.0 137.3 0.835 -0.652\ncore.scoring.hbonds.HBondSet: #D 29 VAL N D 27 HIS O 2.47 111.1 116.9 -152.8 1.000 -0.086\ncore.scoring.hbonds.HBondSet: #D 59 ALA N D 37 GLU OE1 2.23 169.0 99.2 -26.6 0.647 -0.979\ncore.scoring.hbonds.HBondSet: #D 57 ASP N D 38 ASP O 2.02 159.9 148.4 112.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 40 TYR N D 55 ILE O 1.66 150.7 149.5 -0.6 1.000 -0.730\ncore.scoring.hbonds.HBondSet: #D 55 ILE N D 40 TYR O 1.94 155.8 135.9 -80.6 1.000 -0.876\ncore.scoring.hbonds.HBondSet: #D 41 ARG NH2D 54 ASP OD1 2.11 156.8 122.7 133.7 0.647 -1.186\ncore.scoring.hbonds.HBondSet: #D 42 LYS N D 53 LEU O 2.24 133.2 129.7 31.0 1.000 -0.930\ncore.scoring.hbonds.HBondSet: #D 53 LEU N D 42 LYS O 1.82 169.1 144.4 75.9 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #D 42 LYS NZ D 157 TYR OH 2.05 139.6 157.2 168.5 0.812 -0.099\ncore.scoring.hbonds.HBondSet: #D 44 VAL N D 51 CYS O 1.90 142.6 139.5 2.6 1.000 -1.373\ncore.scoring.hbonds.HBondSet: #D 51 CYS N D 44 VAL O 1.71 161.1 161.3 18.3 1.000 -0.780\ncore.scoring.hbonds.HBondSet: #D 46 ILE N D 49 GLU O 1.90 136.6 145.3 -57.8 1.000 -0.553\ncore.scoring.hbonds.HBondSet: #D 49 GLU N D 46 ILE O 2.00 157.3 116.2 99.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 46 ILE O 2.07 136.9 109.4 -56.9 0.765 -0.451\ncore.scoring.hbonds.HBondSet: #D 161 ARG NE D 47 ASP OD2 1.82 167.5 111.8 -159.4 0.718 -1.487\ncore.scoring.hbonds.HBondSet: #D 161 ARG NH2D 47 ASP OD1 1.72 157.2 113.8 147.4 0.718 -1.127\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH1D 47 ASP OD2 2.23 122.1 98.1 -39.4 0.647 -0.042\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 49 GLU OE1 2.08 121.5 136.8 -92.4 0.765 -0.014\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 49 GLU OE1 1.40 140.1 138.2 49.8 0.765 -0.005\ncore.scoring.hbonds.HBondSet: #D 70 GLN N D 67 MET O 2.17 136.5 115.0 -98.6 1.000 -0.317\ncore.scoring.hbonds.HBondSet: #D 72 MET N D 68 ARG O 1.99 166.7 160.7 -170.5 1.000 -1.316\ncore.scoring.hbonds.HBondSet: #D 102 ARG NH1D 69 ASP OD2 2.19 136.9 124.8 139.4 0.459 -0.823\ncore.scoring.hbonds.HBondSet: #D 73 ARG N D 69 ASP O 1.97 140.8 139.1 -103.9 1.000 -0.550\ncore.scoring.hbonds.HBondSet: #D 74 THR N D 70 GLN O 2.16 137.2 131.6 -177.7 1.000 -1.376\ncore.scoring.hbonds.HBondSet: #D 75 GLY N D 72 MET O 2.38 158.1 105.7 -99.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #D 78 PHE N D 110 PRO O 2.05 157.7 144.7 -143.1 1.000 -1.368\ncore.scoring.hbonds.HBondSet: #D 112 VAL N D 78 PHE O 2.10 143.2 152.5 -172.7 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 114 VAL N D 80 CYS O 1.72 164.9 149.5 117.5 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 80 CYS N D 112 VAL O 1.95 161.0 172.9 34.9 1.000 -0.982\ncore.scoring.hbonds.HBondSet: #D 82 PHE N D 114 VAL O 2.03 167.4 170.3 75.0 1.000 -1.069\ncore.scoring.hbonds.HBondSet: #D 116 ASN N D 82 PHE O 2.12 146.4 173.7 -3.8 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #D 86 ASN N D 83 ALA O 2.54 144.5 114.1 -111.9 1.000 -0.035\ncore.scoring.hbonds.HBondSet: #D 83 ALA N D 89 SER OG 2.11 146.5 117.3 152.5 0.976 -1.646\ncore.scoring.hbonds.HBondSet: #D 124 THR N D 84 ILE O 1.93 160.3 139.9 136.2 1.000 -1.379\ncore.scoring.hbonds.HBondSet: #D 125 VAL N D 84 ILE O 2.05 139.0 162.4 -12.1 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #D 84 ILE N D 116 ASN O 1.94 147.6 177.3 -97.9 1.000 -0.661\ncore.scoring.hbonds.HBondSet: #D 89 SER N D 86 ASN OD1 2.00 161.6 108.1 -98.8 0.906 -0.997\ncore.scoring.hbonds.HBondSet: #D 90 PHE N D 86 ASN O 2.32 158.0 145.2 -158.1 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #D 91 GLU N D 87 THR O 1.78 158.6 144.7 -139.2 1.000 -1.110\ncore.scoring.hbonds.HBondSet: #D 88 LYS NZ D 91 GLU OE1 2.12 150.6 156.0 -89.7 0.459 -0.167\ncore.scoring.hbonds.HBondSet: #D 92 ASP N D 88 LYS O 1.73 149.1 145.6 -122.1 1.000 -0.547\ncore.scoring.hbonds.HBondSet: #D 93 ILE N D 90 PHE O 2.03 147.4 105.4 -96.7 1.000 -0.527\ncore.scoring.hbonds.HBondSet: #D 94 HIS N D 91 GLU O 2.28 154.2 119.5 -110.3 1.000 -0.747\ncore.scoring.hbonds.HBondSet: #D 95 GLN N D 92 ASP O 1.97 143.9 112.2 -97.6 1.000 -0.551\ncore.scoring.hbonds.HBondSet: #D 96 TYR N D 92 ASP O 2.30 161.1 156.2 175.1 1.000 -1.118\ncore.scoring.hbonds.HBondSet: #D 97 ARG N D 93 ILE O 2.05 176.1 164.5 -98.8 1.000 -1.133\ncore.scoring.hbonds.HBondSet: #D 98 GLU N D 94 HIS O 2.48 142.6 122.3 -120.3 1.000 -0.261\ncore.scoring.hbonds.HBondSet: #D 99 GLN N D 95 GLN O 1.99 161.3 153.0 -125.4 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 100 ILE N D 96 TYR O 1.87 177.4 169.1 -152.0 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #D 101 LYS N D 97 ARG O 1.86 167.3 142.3 -115.0 1.000 -1.108\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 98 GLU O 2.22 125.0 130.7 -126.1 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 99 GLN O 2.09 133.2 99.1 -93.1 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #D 103 VAL N D 99 GLN O 1.88 169.2 172.6 -128.9 1.000 -1.037\ncore.scoring.hbonds.HBondSet: #D 104 LYS N D 100 ILE O 1.81 170.9 160.9 -48.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 106 SER N D 101 LYS O 2.55 140.0 125.9 -41.0 1.000 -0.377\ncore.scoring.hbonds.HBondSet: #D 108 ASP N D 106 SER OG 2.21 137.3 143.4 13.5 0.459 -0.092\ncore.scoring.hbonds.HBondSet: #D 142 ILE N D 113 LEU O 2.18 165.5 165.0 143.8 1.000 -1.054\ncore.scoring.hbonds.HBondSet: #D 113 LEU N D 140 PRO O 1.99 168.8 165.8 -121.5 1.000 -1.121\ncore.scoring.hbonds.HBondSet: #D 144 THR N D 115 GLY O 2.05 151.3 119.0 102.4 1.000 -0.815\ncore.scoring.hbonds.HBondSet: #D 115 GLY N D 142 ILE O 2.14 152.6 145.4 126.2 1.000 -0.985\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 116 ASN OD1 1.95 135.6 102.0 -56.4 1.000 -0.502\ncore.scoring.hbonds.HBondSet: #D 146 ALA N D 116 ASN OD1 2.50 148.1 139.3 174.2 1.000 -0.040\ncore.scoring.hbonds.HBondSet: #D 120 LEU N D 117 LYS O 1.73 153.1 140.1 -82.7 1.000 -0.460\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 144 THR O 2.23 116.8 127.4 -123.2 1.000 -0.076\ncore.scoring.hbonds.HBondSet: #D 118 CYS N D 144 THR O 1.88 157.5 150.5 118.9 1.000 -0.964\ncore.scoring.hbonds.HBondSet: #D 123 ARG NE D 125 VAL O 1.82 128.0 130.3 143.5 0.624 -0.648\ncore.scoring.hbonds.HBondSet: #D 130 ALA N D 126 GLU O 2.57 166.7 149.2 -153.7 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 128 ARG NH2D 127 SER OG 2.10 123.3 96.6 53.1 0.412 -0.055\ncore.scoring.hbonds.HBondSet: #D 131 GLN N D 127 SER O 1.81 150.8 149.5 -138.0 1.000 -0.911\ncore.scoring.hbonds.HBondSet: #D 132 ASP N D 128 ARG O 1.96 143.7 138.7 -118.4 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #D 133 LEU N D 129 GLN O 2.05 154.0 149.6 -123.9 1.000 -1.006\ncore.scoring.hbonds.HBondSet: #D 134 ALA N D 130 ALA O 2.04 172.6 153.4 -117.2 1.000 -1.210\ncore.scoring.hbonds.HBondSet: #D 135 ARG N D 131 GLN O 2.00 157.8 139.8 -105.8 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 136 SER N D 132 ASP O 1.90 143.1 135.1 -132.5 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 137 TYR N D 133 LEU O 1.93 138.5 144.3 -145.7 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 134 ALA O 2.06 114.7 140.4 -145.1 1.000 -0.403\ncore.scoring.hbonds.HBondSet: #D 139 ILE N D 134 ALA O 1.90 169.0 134.7 69.1 1.000 -1.158\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 135 ARG O 2.19 144.5 99.6 -80.6 1.000 -0.216\ncore.scoring.hbonds.HBondSet: #D 141 TYR OH D 143 GLU OE2 1.45 141.9 141.2 32.0 0.906 -0.834\ncore.scoring.hbonds.HBondSet: #D 148 THR N D 145 SER OG 2.21 162.4 109.0 -94.6 0.718 -1.869\ncore.scoring.hbonds.HBondSet: #D 145 SER N D 150 GLN O 2.05 157.8 160.0 -28.2 1.000 -1.124\ncore.scoring.hbonds.HBondSet: #D 149 ARG N D 145 SER O 2.27 108.0 131.2 -130.5 1.000 0.000\ncore.scoring.hbonds.HBondSet: #D 150 GLN N D 148 THR OG1 2.01 159.2 116.7 54.1 0.553 -1.978\ncore.scoring.hbonds.HBondSet: #D 152 VAL N D 149 ARG O 2.08 167.7 133.5 -113.0 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH1D 153 GLU OE2 1.72 139.9 116.1 110.6 0.624 -0.269\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 153 GLU OE2 2.14 128.3 171.8 -38.7 0.624 -0.141\ncore.scoring.hbonds.HBondSet: #D 155 ALA N D 151 GLY O 2.21 144.4 149.7 -122.7 1.000 -0.640\ncore.scoring.hbonds.HBondSet: #D 156 PHE N D 152 VAL O 2.49 164.9 140.1 -133.1 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #D 157 TYR N D 153 GLU O 1.61 176.4 168.7 -139.5 1.000 -0.343\ncore.scoring.hbonds.HBondSet: #D 159 LEU N D 155 ALA O 2.52 140.7 130.8 -124.7 1.000 -0.182\ncore.scoring.hbonds.HBondSet: #D 160 VAL N D 156 PHE O 2.09 159.7 161.6 -154.7 1.000 -1.128\ncore.scoring.hbonds.HBondSet: #D 161 ARG N D 157 TYR O 2.63 167.6 136.4 -88.2 1.000 -0.115\ncore.scoring.hbonds.HBondSet: #D 162 GLU N D 158 THR O 2.14 149.2 143.1 -142.7 1.000 -1.147\ncore.scoring.hbonds.HBondSet: #D 163 ILE N D 159 LEU O 1.94 160.5 153.2 -126.9 1.000 -1.117\ncore.scoring.hbonds.HBondSet: #D 164 ARG N D 160 VAL O 1.61 159.8 154.1 -143.4 1.000 -0.367\ncore.scoring.hbonds.HBondSet: #D 165 GLN N D 161 ARG O 1.72 164.1 141.9 -98.0 1.000 -0.642\ncore.scoring.hbonds.HBondSet: #D 166 HIS N D 162 GLU O 1.79 161.8 144.1 -107.5 1.000 -0.839\ncore.scoring.hbonds.HBondSet: #D 167 LYS N D 163 ILE O 1.99 160.5 154.2 -112.8 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 168 LEU N D 165 GLN O 2.12 141.5 110.2 -100.9 1.000 -0.446\ncore.scoring.hbonds.HBondSet: #D 169 ARG N D 166 HIS O 1.83 168.3 146.2 -120.5 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #D 170 LYS N D 167 LYS O 2.34 150.5 125.7 -124.0 1.000 -0.782\n#Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\n#A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: false\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: false\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: false\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\n3775.511701096452\nNone\n926\n407\n-1.2098840439684349\n0.10835353848860374\n1.5729435146961963\ncore.import_pose.import_pose: File '../test/data/workshops/1YY9.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 613\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: Found disulfide between residues 6 33\ncore.conformation.Conformation: Found disulfide between residues 132 162\ncore.conformation.Conformation: Found disulfide between residues 165 174\ncore.conformation.Conformation: Found disulfide between residues 169 182\ncore.conformation.Conformation: Found disulfide between residues 190 198\ncore.conformation.Conformation: Found disulfide between residues 194 206\ncore.conformation.Conformation: Found disulfide between residues 207 215\ncore.conformation.Conformation: Found disulfide between residues 211 223\ncore.conformation.Conformation: Found disulfide between residues 226 235\ncore.conformation.Conformation: Found disulfide between residues 239 266\ncore.conformation.Conformation: Found disulfide between residues 270 282\ncore.conformation.Conformation: Found disulfide between residues 286 301\ncore.conformation.Conformation: Found disulfide between residues 304 308\ncore.conformation.Conformation: Found disulfide between residues 312 337\ncore.conformation.Conformation: Found disulfide between residues 445 474\ncore.conformation.Conformation: Found disulfide between residues 481 490\ncore.conformation.Conformation: Found disulfide between residues 485 498\ncore.conformation.Conformation: Found disulfide between residues 501 510\ncore.conformation.Conformation: Found disulfide between residues 514 530\ncore.conformation.Conformation: Found disulfide between residues 533 546\ncore.conformation.Conformation: Found disulfide between residues 537 554\ncore.conformation.Conformation: Found disulfide between residues 557 566\ncore.conformation.Conformation: Found disulfide between residues 570 592\ncore.conformation.Conformation: Found disulfide between residues 595 603\ncore.conformation.Conformation: Found disulfide between residues 599 611\ncore.conformation.Conformation: Found disulfide between residues 636 701\ncore.conformation.Conformation: Found disulfide between residues 747 807\ncore.conformation.Conformation: Found disulfide between residues 846 919\ncore.conformation.Conformation: Found disulfide between residues 970 1026\ncore.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 2 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 138 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 179 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 192 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 193 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 257 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 299 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 502 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 518 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 520 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 522 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 631 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 739 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 801 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 824 because of missing atom number 7 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 959 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 1039 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 1040 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 1044 because of missing atom number 7 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 313 rotamers at 23 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished Workshop3test in 0:00:08.378195", "state": "passed"}, "Workshop4test": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nIteration: 0 Score: 1.977790558838489 Low Score: 1.9387244928752159\nIteration: 1 Score: 2.0097867163563627 Low Score: 1.9387244928752159\nIteration: 2 Score: 2.0097867163563627 Low Score: 1.9387244928752159\nIteration: 3 Score: 2.0097867163563627 Low Score: 1.9387244928752159\nIteration: 4 Score: 5.38036979990547 Low Score: 1.9387244928752159\nIteration: 5 Score: 2.0097867163563627 Low Score: 1.9387244928752159\nIteration: 6 Score: 2.0097867163563627 Low Score: 1.9387244928752159\nIteration: 7 Score: 2.0097867163563627 Low Score: 1.9387244928752159\nIteration: 8 Score: 7.64999014975617 Low Score: 1.9387244928752159\nIteration: 9 Score: 2.464876213054378 Low Score: 1.9387244928752159\nIteration: 10 Score: 2.1479826725554947 Low Score: 1.9387244928752159\nIteration: 11 Score: 10.386339561824382 Low Score: 1.9387244928752159\nIteration: 12 Score: 2.1444565451770856 Low Score: 1.9387244928752159\nIteration: 13 Score: 1.4429280667934234 Low Score: 1.9387244928752159\nIteration: 14 Score: 1.4891647329272582 Low Score: 1.4429280667934234\nIteration: 15 Score: 1.5153185319617766 Low Score: 1.4429280667934234\nIteration: 16 Score: 1.5153185319617766 Low Score: 1.4429280667934234\nIteration: 17 Score: 1.5027474011644646 Low Score: 1.4429280667934234\nIteration: 18 Score: 1.5247901196971494 Low Score: 1.4429280667934234\nIteration: 19 Score: 1.5649245236352236 Low Score: 1.4429280667934234\nIteration: 20 Score: 1.596619197236282 Low Score: 1.4429280667934234\nIteration: 21 Score: 1.3448865764237974 Low Score: 1.4429280667934234\nIteration: 22 Score: 5.050425035641338 Low Score: 1.3448865764237974\nIteration: 23 Score: 1.5041534923668873 Low Score: 1.3448865764237974\nIteration: 24 Score: 1.5041534923668873 Low Score: 1.3448865764237974\nIteration: 25 Score: 1.5176060629211534 Low Score: 1.3448865764237974\nIteration: 26 Score: 1.5423351361629942 Low Score: 1.3448865764237974\nIteration: 27 Score: 1.505973378198612 Low Score: 1.3448865764237974\nIteration: 28 Score: 5.227981810191698 Low Score: 1.3448865764237974\nIteration: 29 Score: 1.4993649318738331 Low Score: 1.3448865764237974\nIteration: 30 Score: 0.7962106029569558 Low Score: 1.3448865764237974\nIteration: 31 Score: 3.676543522104674 Low Score: 0.7962106029569558\nIteration: 32 Score: 0.6609701089700559 Low Score: 0.7962106029569558\nIteration: 33 Score: 8.631683368599177 Low Score: 0.6609701089700559\nIteration: 34 Score: 0.6616698375348697 Low Score: 0.6609701089700559\nIteration: 35 Score: 0.6945422945024635 Low Score: 0.6609701089700559\nIteration: 36 Score: 0.6945422945024635 Low Score: 0.6609701089700559\nIteration: 37 Score: 0.05727758461650012 Low Score: 0.6609701089700559\nIteration: 38 Score: 0.1251429758384175 Low Score: 0.05727758461650012\nIteration: 39 Score: -0.5720107269243764 Low Score: 0.05727758461650012\nIteration: 40 Score: -0.6268704204136766 Low Score: -0.5720107269243764\nIteration: 41 Score: -0.5248395521954485 Low Score: -0.6268704204136766\nIteration: 42 Score: 5.017271710795997 Low Score: -0.6268704204136766\nIteration: 43 Score: -0.48023539207575716 Low Score: -0.6268704204136766\nIteration: 44 Score: 0.7575778023691315 Low Score: -0.6268704204136766\nIteration: 45 Score: -0.7034623985614177 Low Score: -0.6268704204136766\nIteration: 46 Score: -0.7290799842462192 Low Score: -0.7034623985614177\nIteration: 47 Score: -0.5480660576928456 Low Score: -0.7290799842462192\nIteration: 48 Score: 0.42485612807666673 Low Score: -0.7290799842462192\nIteration: 49 Score: 0.46117769694045574 Low Score: -0.7290799842462192\nIteration: 50 Score: 0.4069887845941569 Low Score: -0.7290799842462192\nIteration: 51 Score: 0.38845485492458653 Low Score: -0.7290799842462192\nIteration: 52 Score: 0.5298788283694842 Low Score: -0.7290799842462192\nIteration: 53 Score: 0.570957828974568 Low Score: -0.7290799842462192\nIteration: 54 Score: 0.6104545385181384 Low Score: -0.7290799842462192\nIteration: 55 Score: 0.6104545385181384 Low Score: -0.7290799842462192\nIteration: 56 Score: 0.5935399750848482 Low Score: -0.7290799842462192\nIteration: 57 Score: 0.5935399750848482 Low Score: -0.7290799842462192\nIteration: 58 Score: 0.5263235741138503 Low Score: -0.7290799842462192\nIteration: 59 Score: 0.5263235741138503 Low Score: -0.7290799842462192\nIteration: 60 Score: 0.5817690634400279 Low Score: -0.7290799842462192\nIteration: 61 Score: 0.5817690634400279 Low Score: -0.7290799842462192\nIteration: 62 Score: 2.097871251204607 Low Score: -0.7290799842462192\nIteration: 63 Score: 1.5731480223716199 Low Score: -0.7290799842462192\nIteration: 64 Score: 1.5810319003375293 Low Score: -0.7290799842462192\nIteration: 65 Score: 1.5810319003375293 Low Score: -0.7290799842462192\nIteration: 66 Score: 1.3416922286899027 Low Score: -0.7290799842462192\nIteration: 67 Score: 1.2940649978569976 Low Score: -0.7290799842462192\nIteration: 68 Score: 1.2940649978569976 Low Score: -0.7290799842462192\nIteration: 69 Score: 7.390639665226889 Low Score: -0.7290799842462192\nIteration: 70 Score: 6.456994187199169 Low Score: -0.7290799842462192\nIteration: 71 Score: 1.3576969929127412 Low Score: -0.7290799842462192\nIteration: 72 Score: 1.3322668521507977 Low Score: -0.7290799842462192\nIteration: 73 Score: 1.2236386438346836 Low Score: -0.7290799842462192\nIteration: 74 Score: 1.1681068552499436 Low Score: -0.7290799842462192\nIteration: 75 Score: 1.238598181986358 Low Score: -0.7290799842462192\nIteration: 76 Score: 0.6021658337778968 Low Score: -0.7290799842462192\nIteration: 77 Score: 0.609715702191373 Low Score: -0.7290799842462192\nIteration: 78 Score: 0.6153469903741415 Low Score: -0.7290799842462192\nIteration: 79 Score: 0.5922649360716807 Low Score: -0.7290799842462192\nIteration: 80 Score: 0.7113765269529946 Low Score: -0.7290799842462192\nIteration: 81 Score: -0.3871957459786124 Low Score: -0.7290799842462192\nIteration: 82 Score: -0.38361388833984567 Low Score: -0.7290799842462192\nIteration: 83 Score: -0.1841383911283785 Low Score: -0.7290799842462192\nIteration: 84 Score: -0.3111876842548229 Low Score: -0.7290799842462192\nIteration: 85 Score: -0.42308180652166527 Low Score: -0.7290799842462192\nIteration: 86 Score: -0.42235010607063295 Low Score: -0.7290799842462192\nIteration: 87 Score: -0.5260189964505786 Low Score: -0.7290799842462192\nIteration: 88 Score: -0.5566703987521242 Low Score: -0.7290799842462192\nIteration: 89 Score: -0.7020956322840091 Low Score: -0.7290799842462192\nIteration: 90 Score: -0.6514970124528761 Low Score: -0.7290799842462192\nIteration: 91 Score: -0.6373018756750444 Low Score: -0.7290799842462192\nIteration: 92 Score: -0.6622069285078656 Low Score: -0.7290799842462192\nIteration: 93 Score: -0.21622912961723983 Low Score: -0.7290799842462192\nIteration: 94 Score: -0.26286962938899006 Low Score: -0.7290799842462192\nIteration: 95 Score: -0.3259459032513661 Low Score: -0.7290799842462192\nIteration: 96 Score: -0.3307427156282481 Low Score: -0.7290799842462192\nIteration: 97 Score: -0.3270698258138056 Low Score: -0.7290799842462192\nIteration: 98 Score: 4.022173766118587 Low Score: -0.7290799842462192\nIteration: 99 Score: -0.32719999956697343 Low Score: -0.7290799842462192\n3775.511701096452\nResidue 5: LYS (LYS, K):\nBase: LYS\n Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE METALBINDING SIDECHAIN_AMINE ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB CG CD CE NZ 1HB 2HB 1HG 2HG 1HD 2HD 1HE 2HE 1HZ 2HZ 3HZ \nAtom Coordinates:\n N : 20.315, 43.835, 78.015\n CA : 20.418, 42.863, 79.118\n C : 19.697, 43.46, 80.329\n O : 20.096, 44.486, 80.897\n CB : 21.858, 42.487, 79.491\n CG : 22.791, 42.176, 78.316\n CD : 22.406, 40.943, 77.485\n CE : 23.009, 40.932, 76.075\n NZ : 22.748, 42.169, 75.307\n H : 21.0493, 44.5172, 77.8902\n HA : 19.9193, 41.9417, 78.815\n 1HB : 22.3125, 43.3019, 80.0551\n 2HB : 21.8492, 41.6078, 80.1356\n 1HG : 22.8124, 43.0262, 77.6332\n 2HG : 23.8008, 42.0064, 78.6884\n 1HD : 22.7418, 40.0399, 77.9965\n 2HD : 21.3219, 40.8985, 77.3807\n 1HE : 24.088, 40.801, 76.1421\n 2HE : 22.5982, 40.0953, 75.5101\n 1HZ : 23.1708, 42.0938, 74.3926\n 2HZ : 21.751, 42.2999, 75.2069\n 3HZ : 23.1434, 42.9592, 75.7961\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 5: LYS (LYS, K):\nBase: LYS\n Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE SIDECHAIN_AMINE ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H \n Side-chain atoms: CB CEN\nAtom Coordinates:\n N : 20.315, 43.835, 78.015\n CA : 20.418, 42.863, 79.118\n C : 19.697, 43.46, 80.329\n O : 20.096, 44.486, 80.897\n CB : 21.8754, 42.543, 79.454\n CEN: 23.4957, 41.1851, 79.3707\n H : 21.0493, 44.5172, 77.8902\nMirrored relative to coordinates in ResidueType: FALSE\n\n-104.17784121598451\nResidue 5: LYS (LYS, K):\nBase: LYS\n Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE METALBINDING SIDECHAIN_AMINE ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB CG CD CE NZ 1HB 2HB 1HG 2HG 1HD 2HD 1HE 2HE 1HZ 2HZ 3HZ \nAtom Coordinates:\n N : 20.315, 43.835, 78.015\n CA : 20.418, 42.863, 79.118\n C : 19.697, 43.46, 80.329\n O : 20.096, 44.486, 80.897\n CB : 21.8754, 42.5429, 79.4539\n CG : 22.8944, 43.244, 78.5655\n CD : 22.2113, 44.1202, 77.5262\n CE : 20.6967, 44.0574, 77.6573\n NZ : 20.2706, 43.1587, 78.7642\n H : 21.0493, 44.5172, 77.8902\n HA : 19.9306, 41.9373, 78.8101\n 1HB : 22.0814, 42.8255, 80.4867\n 2HB : 22.0409, 41.4686, 79.3693\n 1HG : 23.5468, 43.8654, 79.1801\n 2HG : 23.5056, 42.4999, 78.0558\n 1HD : 22.5361, 45.154, 77.6512\n 2HD : 22.4937, 43.7874, 76.5274\n 1HE : 20.3065, 45.0564, 77.8461\n 2HE : 20.2655, 43.6934, 76.7248\n 1HZ : 19.2619, 43.1443, 78.8176\n 2HZ : 20.6116, 42.2236, 78.5898\n 3HZ : 20.6485, 43.497, 79.6375\nMirrored relative to coordinates in ResidueType: FALSE\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.05515 seconds.\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.import_pose.import_pose: File '../test/data/workshops/6Q21.clean.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.177533 seconds to load from binary\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.018955 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/workshops/aat000_03_05.200_v1_3\n\nFinished Workshop4test in 0:00:09.145132", "state": "passed"}, "Workshop5test": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\nMover name: PyMOLMover, Mover type: MoverBase, Mover current tag:NoTag\nKeep history: True\nUpdate energy: False\nLast packet sent time: 1.72574e+09\nUpdate interval: 0\nLink: max packet size: 7678\nsent count: 2\nsocket handle: 3\nuuid shorts: 0 0 0 0 0 0 0 0 \nsocket address family: \u0002\nsocket address address: 16777343 : 127.0.0.1\nsocket address port: 59645 : 65000\nsocket max_packet_size: 7678\n\n\nMover name: Small, Mover type: Small, Mover current tag:NoTag\nMax angle for helices (H): 5\nMax angle for strands (E): 5\nMax angle for loops (L): 5\nTemperature factor (kT): 1\nNumber of moves: 1\n\nMover name: Shear, Mover type: Shear, Mover current tag:NoTag\nMax angle for helices (H): 0\nMax angle for strands (E): 5\nMax angle for loops (L): 6\nTemperature factor (kT): 1\nNumber of moves: 1\n\n\n-------------------------------\n resnum Type TRUE/FALSE \n-------------------------------\n DEFAULT BB FALSE\n DEFAULT SC FALSE\n DEFAULT NU FALSE\n DEFAULT BRANCH FALSE\n 050 BB TRUE\n 051 BB TRUE\n-------------------------------\n jumpnum Type TRUE/FALSE \n-------------------------------\n DEFAULT JUMP FALSE\n-------------------------------\n resnum atomnum Type TRUE/FALSE \n-------------------------------\n DEFAULT PHI FALSE\n DEFAULT THETA FALSE\n DEFAULT D FALSE\n DEFAULT RB1 FALSE\n DEFAULT RB2 FALSE\n DEFAULT RB3 FALSE\n DEFAULT RB4 FALSE\n DEFAULT RB5 FALSE\n DEFAULT RB6 FALSE\n-------------------------------\n\n\nMover name: MinMover, Mover type: MinMover, Mover current tag:NoTag\nMinimization type:\tlbfgs_armijo_nonmonotone\nScorefunction:\t\tref2015\nScore tolerance:\t0.01\nNb list:\t\tTrue\nDeriv check:\t\tFalse\nMovemap:\n\n-------------------------------\n resnum Type TRUE/FALSE \n-------------------------------\n DEFAULT BB FALSE\n DEFAULT SC FALSE\n DEFAULT NU FALSE\n DEFAULT BRANCH FALSE\n 040 BB TRUE\n 041 BB TRUE\n 042 BB TRUE\n 043 BB TRUE\n 044 BB TRUE\n 045 BB TRUE\n 046 BB TRUE\n 047 BB TRUE\n 048 BB TRUE\n 049 BB TRUE\n 050 BB TRUE\n 051 BB TRUE\n 052 BB TRUE\n 053 BB TRUE\n 054 BB TRUE\n 055 BB TRUE\n 056 BB TRUE\n 057 BB TRUE\n 058 BB TRUE\n 059 BB TRUE\n 060 BB TRUE\n-------------------------------\n jumpnum Type TRUE/FALSE \n-------------------------------\n DEFAULT JUMP FALSE\n-------------------------------\n resnum atomnum Type TRUE/FALSE \n-------------------------------\n DEFAULT PHI FALSE\n DEFAULT THETA FALSE\n DEFAULT D FALSE\n DEFAULT RB1 FALSE\n DEFAULT RB2 FALSE\n DEFAULT RB3 FALSE\n DEFAULT RB4 FALSE\n DEFAULT RB5 FALSE\n DEFAULT RB6 FALSE\n-------------------------------\n\n\n1\n0.5\nMover name: SequenceMover, Mover type: MoverBase, Mover current tag: NoTag\n3 movers are contained in the following order:\n Mover[1]: Small\n Mover[2]: Shear\n Mover[3]: MinMover\n\nMover name: TrialMover, Mover type: MoverBase, Mover current tag: NoTag\nMover being tried: 0x600007cfd5e0\nMoves were accepted: 0 times.\nAcceptance rate: 0\nMonteCarlo: 0x600007da7740\n\nMover name: RepeatMover, Mover type: RepeatMover, Mover current tag: NoTag\nMover being repeated: TrialMover, nmoves: 2\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.943937 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.203322 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 142.844 142.844\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.moves.MonteCarlo: MC: 1 142.844 142.844 142.844 142.844 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.TrialMover: Acceptance rate: 0.5\nprotocols.moves.MonteCarlo: MC: 1 -245.18 -245.18 -245.18 -245.18 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: Small trials= 2; accepts= 0.5000; energy_drop/trial= -194.01213\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.moves.MonteCarlo: MC: 1 -303.474 -303.474 -303.474 -303.474 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: Small trials= 2; accepts= 0.5000; energy_drop/trial= -194.01213\nprotocols.moves.TrialCounter: SmallShearMinMov trials= 2; accepts= 1.0000; energy_drop/trial= -29.14699\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.relax.ClassicRelax: Setting up default relax setting\n\nFinished Workshop5test in 0:00:12.365221", "state": "passed"}, "Workshop6test": {"log": "\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 PyRosetta-4 \u2502\n\u2502 Created in JHU by Sergey Lyskov and PyRosetta Team \u2502\n\u2502 (C) Copyright Rosetta Commons Member Institutions \u2502\n\u2502 \u2502\n\u2502 NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE \u2502\n\u2502 See LICENSE.PyRosetta.md or email license@uw.edu for details \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\nPyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git\n#Packer_Task\n\nThreads to request: ALL 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SE\tFALSE\tLYS\n625\tFALSE\tFALSE\tVAL\n626\tFALSE\tFALSE\tTYR\n627\tFALSE\tFALSE\tALA\n628\tFALSE\tFALSE\t\n629\tFALSE\tFALSE\tGLU\n630\tFALSE\tFALSE\tVAL\n631\tFALSE\tFALSE\tTHR\n632\tFALSE\tFALSE\tHIS,HIS_D\n633\tFALSE\tFALSE\tGLN\n634\tFALSE\tFALSE\tGLY\n635\tFALSE\tFALSE\tLEU\n636\tFALSE\tFALSE\tSER\n637\tFALSE\tFALSE\tSER\n638\tFALSE\tFALSE\tPRO\n639\tFALSE\tFALSE\tVAL\n640\tFALSE\tFALSE\tTHR\n641\tFALSE\tFALSE\tLYS\n642\tFALSE\tFALSE\tSER\n643\tFALSE\tFALSE\tPHE\n644\tFALSE\tFALSE\tASN\n645\tFALSE\tFALSE\tARG\n646\tFALSE\tFALSE\tGLY\n647\tFALSE\tFALSE\tALA:CtermProteinFull\n648\tFALSE\tFALSE\tGLN:NtermProteinFull\n649\tFALSE\tFALSE\tVAL\n650\tFALSE\tFALSE\tGLN\n651\tFALSE\tFALSE\tLEU\n652\tFALSE\tFALSE\tLYS\n653\tFALSE\tFALSE\tGLN\n654\tFALSE\tFALSE\tSER\n655\tFALSE\tFALSE\tGLY\n656\tFALSE\tFALSE\tPRO\n657\tFALSE\tFALSE\tGLY\n658\tFALSE\tFALSE\tLEU\n659\tFALSE\tFALSE\tVAL\n660\tFALSE\tFALSE\tGLN\n661\tFALSE\tFALSE\tPRO\n662\tFALSE\tFALSE\tSER\n663\tFALSE\tFALSE\tGLN\n664\tFALSE\tFALSE\tSER\n665\tFALSE\tFALSE\tLEU\n666\tFALSE\tFALSE\tSER\n667\tFALSE\tFALSE\tILE\n668\tFALSE\tFALSE\tTHR\n669\tFALSE\tFALSE\t\n670\tFALSE\tFALSE\tTHR\n671\tFALSE\tFALSE\tVAL\n672\tFALSE\tFALSE\tSER\n673\tFALSE\tFALSE\tGLY\n674\tFALSE\tFALSE\tPHE\n675\tFALSE\tFALSE\tSER\n676\tFALSE\tFALSE\tLEU\n677\tFALSE\tFALSE\tTHR\n678\tFALSE\tFALSE\tASN\n679\tFALSE\tFALSE\tTYR\n680\tFALSE\tFALSE\tGLY\n681\tFALSE\tFALSE\tVAL\n682\tFALSE\tFALSE\tHIS,HIS_D\n683\tFALSE\tFALSE\tTRP\n684\tFALSE\tFALSE\tVAL\n685\tFALSE\tFALSE\tARG\n686\tFALSE\tFALSE\tGLN\n687\tFALSE\tFALSE\tSER\n688\tFALSE\tFALSE\tPRO\n689\tFALSE\tFALSE\tGLY\n690\tFALSE\tFALSE\tLYS\n691\tFALSE\tFALSE\tGLY\n692\tFALSE\tFALSE\tLEU\n693\tFALSE\tFALSE\tGLU\n694\tFALSE\tFALSE\tTRP\n695\tFALSE\tFALSE\tLEU\n696\tFALSE\tFALSE\tGLY\n697\tFALSE\tFALSE\tVAL\n698\tFALSE\tFALSE\tILE\n699\tFALSE\tFALSE\tTRP\n700\tFALSE\tFALSE\tSER\n701\tFALSE\tFALSE\tGLY\n702\tFALSE\tFALSE\tGLY\n703\tFALSE\tFALSE\tASN\n704\tFALSE\tFALSE\tTHR\n705\tFALSE\tFALSE\tASP\n706\tFALSE\tFALSE\tTYR\n707\tFALSE\tFALSE\tASN\n708\tFALSE\tFALSE\tTHR\n709\tFALSE\tFALSE\tPRO\n710\tFALSE\tFALSE\tPHE\n711\tFALSE\tFALSE\tTHR\n712\tFALSE\tFALSE\tSER\n713\tFALSE\tFALSE\tARG\n714\tFALSE\tFALSE\tLEU\n715\tFALSE\tFALSE\tSER\n716\tFALSE\tFALSE\tILE\n717\tFALSE\tFALSE\tASN\n718\tFALSE\tFALSE\tLYS\n719\tFALSE\tFALSE\tASP\n720\tFALSE\tFALSE\tASN\n721\tFALSE\tFALSE\tSER\n722\tFALSE\tFALSE\tLYS\n723\tFALSE\tFALSE\tSER\n724\tFALSE\tFALSE\tGLN\n725\tFALSE\tFALSE\tVAL\n726\tFALSE\tFALSE\tPHE\n727\tFALSE\tFALSE\tPHE\n728\tFALSE\tFALSE\tLYS\n729\tFALSE\tFALSE\tMET\n730\tFALSE\tFALSE\tASN\n731\tFALSE\tFALSE\tSER\n732\tFALSE\tFALSE\tLEU\n733\tFALSE\tFALSE\tGLN\n734\tFALSE\tFALSE\tSER\n735\tFALSE\tFALSE\tASN\n736\tFALSE\tFALSE\tASP\n737\tFALSE\tFALSE\tTHR\n738\tFALSE\tFALSE\tALA\n739\tFALSE\tFALSE\tILE\n740\tFALSE\tFALSE\tTYR\n741\tFALSE\tFALSE\tTYR\n742\tFALSE\tFALSE\t\n743\tFALSE\tFALSE\tALA\n744\tFALSE\tFALSE\tARG\n745\tFALSE\tFALSE\tALA\n746\tFALSE\tFALSE\tLEU\n747\tFALSE\tFALSE\tTHR\n748\tFALSE\tFALSE\tTYR\n749\tFALSE\tFALSE\tTYR\n750\tFALSE\tFALSE\tASP\n751\tFALSE\tFALSE\tTYR\n752\tFALSE\tFALSE\tGLU\n753\tFALSE\tFALSE\tPHE\n754\tFALSE\tFALSE\tALA\n755\tFALSE\tFALSE\tTYR\n756\tFALSE\tFALSE\tTRP\n757\tFALSE\tFALSE\tGLY\n758\tFALSE\tFALSE\tGLN\n759\tFALSE\tFALSE\tGLY\n760\tFALSE\tFALSE\tTHR\n761\tFALSE\tFALSE\tLEU\n762\tFALSE\tFALSE\tVAL\n763\tFALSE\tFALSE\tTHR\n764\tFALSE\tFALSE\tVAL\n765\tFALSE\tFALSE\tSER\n766\tFALSE\tFALSE\tALA\n767\tFALSE\tFALSE\tALA\n768\tFALSE\tFALSE\tSER\n769\tFALSE\tFALSE\tTHR\n770\tFALSE\tFALSE\tLYS\n771\tFALSE\tFALSE\tGLY\n772\tFALSE\tFALSE\tPRO\n773\tFALSE\tFALSE\tSER\n774\tFALSE\tFALSE\tVAL\n775\tFALSE\tFALSE\tPHE\n776\tFALSE\tFALSE\tPRO\n777\tFALSE\tFALSE\tLEU\n778\tFALSE\tFALSE\tALA\n779\tFALSE\tFALSE\tPRO\n780\tFALSE\tFALSE\tSER\n781\tFALSE\tFALSE\tSER\n782\tFALSE\tFALSE\tLYS\n783\tFALSE\tFALSE\tSER\n784\tFALSE\tFALSE\tTHR\n785\tFALSE\tFALSE\tSER\n786\tFALSE\tFALSE\tGLY\n787\tFALSE\tFALSE\tGLY\n788\tFALSE\tFALSE\tTHR\n789\tFALSE\tFALSE\tALA\n790\tFALSE\tFALSE\tALA\n791\tFALSE\tFALSE\tLEU\n792\tFALSE\tFALSE\tGLY\n793\tFALSE\tFALSE\t\n794\tFALSE\tFALSE\tLEU\n795\tFALSE\tFALSE\tVAL\n796\tFALSE\tFALSE\tLYS\n797\tFALSE\tFALSE\tASP\n798\tFALSE\tFALSE\tTYR\n799\tFALSE\tFALSE\tPHE\n800\tFALSE\tFALSE\tPRO\n801\tFALSE\tFALSE\tGLU\n802\tFALSE\tFALSE\tPRO\n803\tFALSE\tFALSE\tVAL\n804\tFALSE\tFALSE\tTHR\n805\tFALSE\tFALSE\tVAL\n806\tFALSE\tFALSE\tSER\n807\tFALSE\tFALSE\tTRP\n808\tFALSE\tFALSE\tASN\n809\tFALSE\tFALSE\tSER\n810\tFALSE\tFALSE\tGLY\n811\tFALSE\tFALSE\tALA\n812\tFALSE\tFALSE\tLEU\n813\tFALSE\tFALSE\tTHR\n814\tFALSE\tFALSE\tSER\n815\tFALSE\tFALSE\tGLY\n816\tFALSE\tFALSE\tVAL\n817\tFALSE\tFALSE\tHIS,HIS_D\n818\tFALSE\tFALSE\tTHR\n819\tFALSE\tFALSE\tPHE\n820\tFALSE\tFALSE\tPRO\n821\tFALSE\tFALSE\tALA\n822\tFALSE\tFALSE\tVAL\n823\tFALSE\tFALSE\tLEU\n824\tFALSE\tFALSE\tGLN\n825\tFALSE\tFALSE\tSER\n826\tFALSE\tFALSE\tSER\n827\tFALSE\tFALSE\tGLY\n828\tFALSE\tFALSE\tLEU\n829\tFALSE\tFALSE\tTYR\n830\tFALSE\tFALSE\tSER\n831\tFALSE\tFALSE\tLEU\n832\tFALSE\tFALSE\tSER\n833\tFALSE\tFALSE\tSER\n834\tFALSE\tFALSE\tVAL\n835\tFALSE\tFALSE\tVAL\n836\tFALSE\tFALSE\tTHR\n837\tFALSE\tFALSE\tVAL\n838\tFALSE\tFALSE\tPRO\n839\tFALSE\tFALSE\tSER\n840\tFALSE\tFALSE\tSER\n841\tFALSE\tFALSE\tSER\n842\tFALSE\tFALSE\tLEU\n843\tFALSE\tFALSE\tGLY\n844\tFALSE\tFALSE\tTHR\n845\tFALSE\tFALSE\tGLN\n846\tFALSE\tFALSE\tTHR\n847\tFALSE\tFALSE\tTYR\n848\tFALSE\tFALSE\tILE\n849\tFALSE\tFALSE\t\n850\tFALSE\tFALSE\tASN\n851\tFALSE\tFALSE\tVAL\n852\tFALSE\tFALSE\tASN\n853\tFALSE\tFALSE\tHIS,HIS_D\n854\tFALSE\tFALSE\tLYS\n855\tFALSE\tFALSE\tPRO\n856\tFALSE\tFALSE\tSER\n857\tFALSE\tFALSE\tASN\n858\tFALSE\tFALSE\tTHR\n859\tFALSE\tFALSE\tLYS\n860\tFALSE\tFALSE\tVAL\n861\tFALSE\tFALSE\tASP\n862\tFALSE\tFALSE\tLYS\n863\tFALSE\tFALSE\tARG\n864\tFALSE\tFALSE\tVAL\n865\tFALSE\tFALSE\tGLU\n866\tFALSE\tFALSE\tPRO\n867\tFALSE\tFALSE\tLYS\n868\tFALSE\tFALSE\tSER:CtermProteinFull\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.956503 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.22122 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 9 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 452 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 648 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 16 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\n\nFinished Workshop6test in 0:00:07.977831", "state": "passed"}, "Workshop7test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed864b cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30\ncore.init: Rosetta extras: []\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.03455 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/complex.start.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 246\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 247\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 247\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 321\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 321\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 321\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 335\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 335\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 335\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 338\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 338\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 338\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 359\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 359\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 359\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 371\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 371\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 371\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 372\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 372\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 372\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 381\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 381\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 381\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 392\ncore.conformation.Conformation: Found disulfide between residues 7 137\ncore.conformation.Conformation: Found disulfide between residues 25 41\ncore.conformation.Conformation: Found disulfide between residues 109 210\ncore.conformation.Conformation: Found disulfide between residues 116 183\ncore.conformation.Conformation: Found disulfide between residues 148 162\ncore.conformation.Conformation: Found disulfide between residues 173 197\ncore.conformation.Conformation: Found disulfide between residues 262 309\ncore.conformation.Conformation: Found disulfide between residues 356 361\ncore.pack.pack_missing_sidechains: packing residue number 246 because of missing atom number 8 atom name CD1\ncore.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 6 atom name OG1\ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 321 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 334 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 335 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 338 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 348 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 359 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 360 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 371 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 372 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 381 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 383 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Volumes/scratch/b3.w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.6-x86_64-i386-64bit/clang-14.0.0/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.193306 seconds to load from binary\ncore.pack.pack_rotamers: built 209 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nprotocols.docking.DockingInitialPerturbation: Sliding Pose components together into contact\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.018695 seconds.\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.46\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body