Test: gcc-9.gcc.serialization.python37.PyRosetta.notebook 「view this page in B3 βῆτα server」
Branch: master 「revision: №61938」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-1     Started at: 2022-09-15 17:45:00     Run time: 1:11:09      State: failed

Failed sub-tests (click for more details):
02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration 15.02-Membrane-Protein-ddG-of-mutation

Test Log

Sub-Tests Results

All sub-tests

01.00-How-to-Get-Started 01.01-How-to-Get-Local-PyRosetta 01.02-Notebooks-Python-Colab 01.03-FAQ 02.00-Introduction-to-PyRosetta 02.01-Pose-Basics 02.02-Working-with-Pose-Residues 02.03-Accessing-PyRosetta-Documentation 02.04-Getting-Spatial-Features-from-Pose 02.05-Protein-Geometry 02.06-Visualization-and-PyMOL-Mover 02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration 02.07-RosettaScripts-in-PyRosetta 02.08-Visualization-and-pyrosetta.distributed.viewer 03.00-Rosetta-Energy-Score-Functions 03.01-Score-Function-Basics 03.02-Analyzing-energy-between-residues 03.03-Energies-and-the-PyMOLMover 04.00-Introduction-to-Folding 04.01-Basic-Folding-Algorithm 04.02-Low-Res-Scoring-and-Fragments 05.00-Structure-Refinement 05.01-High-Res-Movers 05.02-Refinement-Protocol 06.00-Introduction-to-Packing-and-Design 06.01-Side-Chain-Conformations-and-Dunbrack-Energies 06.02-Packing-design-and-regional-relax 06.03-Design-with-a-resfile-and-relax 06.04-Protein-Design-2 06.05-HBNet-Before-Design 06.06-Introduction-to-Parametric-backbone-design 06.07-Introduction-to-DeNovo-protein-design 06.08-Point-Mutation-Scan 07.00-Protein-Docking 07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK 07.02-Docking-Moves-in-Rosetta 08.00-Ligand-Docking-PyRosetta 08.01-Ligand-Docking-XMLObjects 08.02-Ligand-Docking-pyrosetta.distributed 10.00-Working-With-Symmetry 11.00-Working-With-Density 12.00-Working-With-Antibodies 12.01-RosettaAntibody-Framework-and-SimpleMetrics 12.02-RosettaAntibodyDesign-RAbD 13.00-RosettaCarbohydrates-Working-with-Glycans 13.01-Glycan-Trees-Selectors-and-Movers 13.02-Glycan-Modeling-and-Design 14.00-RNA-Basics 15.00-Modeling-Membrane-Proteins 15.01-Accounting-for-the-lipid-bilayer 15.02-Membrane-Protein-ddG-of-mutation 16.00-Running-PyRosetta-in-Parallel 16.01-PyData-ddG-pssm 16.02-PyData-miniprotein-design 16.03-GNU-Parallel-Via-Slurm 16.04-dask.delayed-Via-Slurm 16.05-Ligand-Docking-dask 16.06-PyRosettaCluster-Simple-protocol 16.07-PyRosettaCluster-Reproduce-simple-protocol 16.08-PyRosettaCluster-Multiple-protocols 16.09-PyRosettaCluster-Multiple-decoys 16.10-PyRosettaCluster-Ligand-params A.00-Appendix-A B.00-Appendix-B C.00-Appendix-C D.00-Appendix-D

JSON output

{"tests": {"01.00-How-to-Get-Started": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 01.00-How-to-Get-Started.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 01.00-How-to-Get-Started.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2027509002 seed_offset=0 real_seed=-2027509002\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2027509002 RG_type=mt19937\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1162053471 seed_offset=0 real_seed=1162053471\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1162053471 RG_type=mt19937\n[NbConvertApp] Converting notebook 01.00-How-to-Get-Started.ipynb to python\n[NbConvertApp] Writing 7754 bytes to 01.00-How-to-Get-Started.py\n/bin/sh: 1: pip: not found\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "01.01-How-to-Get-Local-PyRosetta": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 01.01-How-to-Get-Local-PyRosetta.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 01.01-How-to-Get-Local-PyRosetta.py\n[NbConvertApp] Converting notebook 01.01-How-to-Get-Local-PyRosetta.ipynb to python\n[NbConvertApp] Writing 2704 bytes to 01.01-How-to-Get-Local-PyRosetta.py\n", "state": "passed"}, "01.02-Notebooks-Python-Colab": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 01.02-Notebooks-Python-Colab.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 01.02-Notebooks-Python-Colab.py\n[NbConvertApp] Converting notebook 01.02-Notebooks-Python-Colab.ipynb to python\n[NbConvertApp] Writing 2316 bytes to 01.02-Notebooks-Python-Colab.py\n", "state": "passed"}, "01.03-FAQ": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 01.03-FAQ.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 01.03-FAQ.py\n[NbConvertApp] Converting notebook 01.03-FAQ.ipynb to python\n[NbConvertApp] Writing 3134 bytes to 01.03-FAQ.py\n", "state": "passed"}, "02.00-Introduction-to-PyRosetta": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.00-Introduction-to-PyRosetta.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.00-Introduction-to-PyRosetta.py\n[NbConvertApp] Converting notebook 02.00-Introduction-to-PyRosetta.ipynb to python\n[NbConvertApp] Writing 3212 bytes to 02.00-Introduction-to-PyRosetta.py\n", "state": "passed"}, "02.01-Pose-Basics": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.01-Pose-Basics.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.01-Pose-Basics.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1782356646 seed_offset=0 real_seed=-1782356646\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1782356646 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=552872511 seed_offset=0 real_seed=552872511\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=552872511 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.57496 seconds.\ncore.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520\ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 454 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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.283565 seconds to load from binary\ncore.pack.pack_rotamers: built 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File 'inputs/5tj3.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 349\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 349\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 349\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 352\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 352\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 352\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 352\ncore.conformation.Conformation: [ WPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nARNING ] missing heavyatom: CG on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 381\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 TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 519\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 349 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 352 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 381 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 453 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 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 02.01-Pose-Basics.ipynb to python\n[NbConvertApp] Writing 5742 bytes to 02.01-Pose-Basics.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "02.02-Working-with-Pose-Residues": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.02-Working-with-Pose-Residues.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.02-Working-with-Pose-Residues.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=560033069 seed_offset=0 real_seed=560033069\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=560033069 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=558248747 seed_offset=0 real_seed=558248747\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=558248747 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.61267 seconds.\ncore.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520\ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 454 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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.315482 seconds to load from binary\ncore.pack.pack_rotamers: built 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File 'inputs/5tj3.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 349\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 349\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 349\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 352\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 352\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 352\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 352\ncore.conformation.Conformation: [ WPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n524\n519\nASP\nA\n47\n1\n24 A \nARG\nTrue\nARNING ] missing heavyatom: CG on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 381\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 TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 453\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 519\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 349 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 352 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 381 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 453 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 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 02.02-Working-with-Pose-Residues.ipynb to python\n[NbConvertApp] Writing 4515 bytes to 02.02-Working-with-Pose-Residues.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "02.03-Accessing-PyRosetta-Documentation": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.03-Accessing-PyRosetta-Documentation.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.03-Accessing-PyRosetta-Documentation.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1514245478 seed_offset=0 real_seed=-1514245478\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1514245478 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1957510626 seed_offset=0 real_seed=-1957510626\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1957510626 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.74712 seconds.\ncore.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520\ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 454 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoriPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nng.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.29254 seconds to load from binary\ncore.pack.pack_rotamers: built 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 02.03-Accessing-PyRosetta-Documentation.ipynb to python\n[NbConvertApp] Writing 3697 bytes to 02.03-Accessing-PyRosetta-Documentation.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "02.04-Getting-Spatial-Features-from-Pose": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.04-Getting-Spatial-Features-from-Pose.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.04-Getting-Spatial-Features-from-Pose.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-619032493 seed_offset=0 real_seed=-619032493\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-619032493 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1644428123 seed_offset=0 real_seed=-1644428123\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1644428123 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.871 seconds.\ncore.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520\ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 454 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoringPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nphi: -149.17513487055064\npsi: 151.30037995499168\nchi1: -82.85078566898203\n atomno= 1 rsd= 5 \n1.456100614655453\n1.5184027792387658\n1.456100614655453\n1.5184027792387658\n.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.275026 seconds to load from binary\ncore.pack.pack_rotamers: built 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 02.04-Getting-Spatial-Features-from-Pose.ipynb to python\n[NbConvertApp] Writing 5606 bytes to 02.04-Getting-Spatial-Features-from-Pose.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "02.05-Protein-Geometry": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.05-Protein-Geometry.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.05-Protein-Geometry.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1090881398 seed_offset=0 real_seed=1090881398\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1090881398 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-572904868 seed_offset=0 real_seed=-572904868\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-572904868 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.70648 seconds.\ncore.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520\ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 454 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nV\n1.458004\n1.52326\n1.9131887665773852\noriginal phi: 180.0\noriginal psi: 180.0\nxyz coordinates: 3.535270304899898 3.659035776744377 1.199094204197625\nnew phi: -60.0\nnew psi: -43.0\nxyz coordinates: 5.498535447297188 2.671616235800967 0.06968570437453583\nPDB file name: inputs/5tj3.pdb\nTotal residues: 524\nSequence: NAVPRPKLVVGLVVDQMRWDYLYRYYSKYGEGGFKRMLNTGYSLNNVHIDYVPTVTAIGHTSIFTGSVPSIHGIAGNDWYDKELGKSVYCTSDETVQPVGTTSNSVGQHSPRNLWSTTVTDQLGLATNFTSKVVGVSLKDRASILPAGHNPTGAFWFDDTTGKFITSTYYTKELPKWVNDFNNKNVPAQLVANGWNTLLPINQYTESSEDNVEWEGLLGSKKTPTFPYTDLAKDYEAKKGLIRTTPFGNTLTLQMADAAIDGNQMGVDDITDFLTVNLASTDYVGHNFGPNSIEVEDTYLRLDRDLADFFNNLDKKVGKGNYLVFLSADHGAAHSVGFMQAHKMPTGFFDMKKEMNAKLKQKFGADNIIAAAMNYQVYFDRKVLADSKLELDDVRDYVMTELKKEPSVLYVLSTDEIWESSIPEPIKSRVINGYNWKRSGDIQIISKDGYLSAYSKKGTTHSVWNSYDSHIPLLFMGWGIKQGESNQPYHMTDIAPTVSSLLKIQFPSGAVGKPITEVIGZZZZ\nFold tree:\nFOLD_TREE EDGE 1 520 -1 EDGE 1 521 1 EDGE 1 522 2 EDGE 1 523 3 EDGE 1 524 4 \nScoreFunctionFactory: 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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.305559 seconds to load from binary\ncore.pack.pack_rotamers: built 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 02.05-Protein-Geometry.ipynb to python\n[NbConvertApp] Writing 6611 bytes to 02.05-Protein-Geometry.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "02.06-Visualization-and-PyMOL-Mover": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.06-Visualization-and-PyMOL-Mover.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.06-Visualization-and-PyMOL-Mover.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-870414185 seed_offset=0 real_seed=-870414185\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-870414185 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=320707868 seed_offset=0 real_seed=320707868\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=320707868 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.80954 seconds.\ncore.import_pose.import_pose: File 'inputs/5tj3.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 233\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 350\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 353\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 354\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 382\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OH on residue TYR 454\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLY:CtermProteinFull 520\ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 350 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 353 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 354 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 382 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 454 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\noriginal phi: 180.0\noriginal psi: 180.0\nxyz coordinates: 3.535270304899898 3.659035776744377 1.199094204197625\nnew phi: -60.0\nnew psi: -43.0\nxyz coordinates: 5.498535447297188 2.671616235800967 0.06968570437453583\nreFunctionFactory: 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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.365091 seconds to load from binary\ncore.pack.pack_rotamers: built 90 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 02.06-Visualization-and-PyMOL-Mover.ipynb to python\n[NbConvertApp] Writing 8764 bytes to 02.06-Visualization-and-PyMOL-Mover.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.py\n[NbConvertApp] Converting notebook 02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.ipynb to python\n[NbConvertApp] ERROR | Notebook JSON is invalid: data.cells[{data__cells_x}] must be valid exactly by one definition (0 matches found)\n\nFailed validating <unset> in notebook['data']['cells']:\n\nOn instance:\n<unset>\n[NbConvertApp] ERROR | Notebook is invalid after preprocessor <nbconvert.preprocessors.tagremove.TagRemovePreprocessor object at 0x7f159714af50>\nTraceback (most recent call last):\n File \"/home/benchmark/prefix/nobu-1/gcc-9/python-3.7.gcc/97da995822dbf0e01ad4322567219cef/lib/python3.7/runpy.py\", line 193, in _run_module_as_main\n \"__main__\", mod_spec)\n File \"/home/benchmark/prefix/nobu-1/gcc-9/python-3.7.gcc/97da995822dbf0e01ad4322567219cef/lib/python3.7/runpy.py\", line 85, in _run_code\n exec(code, run_globals)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/__main__.py\", line 3, in <module>\n main()\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/jupyter_core/application.py\", line 269, in launch_instance\n return super().launch_instance(argv=argv, **kwargs)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/traitlets/config/application.py\", line 978, in launch_instance\n app.start()\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/nbconvertapp.py\", line 426, in start\n self.convert_notebooks()\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/nbconvertapp.py\", line 600, in convert_notebooks\n self.convert_single_notebook(notebook_filename)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/nbconvertapp.py\", line 564, in convert_single_notebook\n notebook_filename, resources, input_buffer=input_buffer\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/nbconvertapp.py\", line 492, in export_single_notebook\n notebook_filename, resources=resources\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/exporters/exporter.py\", line 190, in from_filename\n return self.from_file(f, resources=resources, **kw)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/exporters/exporter.py\", line 208, in from_file\n nbformat.read(file_stream, as_version=4), resources=resources, **kw\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py\", line 386, in from_notebook_node\n nb_copy, resources = super().from_notebook_node(nb, resources, **kw)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/exporters/exporter.py\", line 147, in from_notebook_node\n nb_copy, resources = self._preprocess(nb_copy, resources)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/exporters/exporter.py\", line 344, in _preprocess\n self._validate_preprocessor(nbc, preprocessor)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbconvert/exporters/exporter.py\", line 311, in _validate_preprocessor\n nbformat.validate(nbc)\n File \"/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/nbformat/validator.py\", line 503, in validate\n raise error\nnbformat.validator.NotebookValidationError: data.cells[{data__cells_x}] must be valid exactly by one definition (0 matches found)\n\nFailed validating <unset> in notebook['data']['cells']:\n\nOn instance:\n<unset>\n", "state": "failed"}, "02.07-RosettaScripts-in-PyRosetta": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.07-RosettaScripts-in-PyRosetta.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.07-RosettaScripts-in-PyRosetta.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1329612614 seed_offset=0 real_seed=1329612614\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1329612614 RG_type=mt19937\ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -no_fconfig @inputs/rabd/common -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1888630243 seed_offset=0 real_seed=-1888630243\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1888630243 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.77399 seconds.\ncore.import_pose.import_pose: File 'inputs/rabd/my_ab.pdb' automatically determined to be of type PDB\ncore.io.pdb.pdb_reader: Parsing 993 .pdb records with unknown format to search for Rosetta-specific comments.\ncore.conformation.Conformation: Found disulfide between residues 771 845\ncore.conformation.Conformation: current variant for 771 CYS\ncore.conformation.Conformation: current variant for 845 CYS\ncore.conformation.Conformation: current variant for 771 CYD\ncore.conformation.Conformation: current variant for 845 CYD\ncore.conformation.Conformation: Found disulfide between residues 891 956\ncore.conformation.Conformation: current variant for 891 CYS\ncore.conformation.Conformation: current variant for 956 CYS\ncore.conformation.Conformation: current variant for 891 CYD\ncore.conformation.Conformation: current variant for 956 CYD\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<SCOREFXNS/>\n\t<RESIDUE_SELECTORS>\n\t\t<CDR cdrs=\"L1\" name=\"L1\"/>\n\t</RESIDUE_SELECTORS>\n\t<MOVE_MAP_FACTORIES>\n\t\t<MoveMapFactory bb=\"0\" chi=\"0\" name=\"movemap_L1\">\n\t\t\t<Backbone residue_selector=\"L1\"/>\n\t\t\t<Chi residue_selector=\"L1\"/>\n\t\t</MoveMapFactory>\n\t</MOVE_MAP_FACTORIES>\n\t<SIMPLE_METRICS>\n\t\t<TimingProfileMetric name=\"timing\"/>\n\t\t<SelectedResiduesMetric name=\"rosetta_sele\" residue_selector=\"L1\" rosetta_numbering=\"1\"/>\n\t\t<SelectedResiduesPyMOLMetric name=\"pymol_selection\" residue_selector=\"L1\"/>\n\t\t<SequenceMetric name=\"sequence\" residue_selector=\"L1\"/>\n\t\t<SecondaryStructureMetric name=\"ss\" residue_selector=\"L1\"/>\n\t</SIMPLE_METRICS>\n\t<MOVERS>\n\t\t<MinMover movemap_factory=\"movemap_L1\" name=\"min_mover\" tolerance=\".1\"/>\n\t\t<RunSimpleMetrics metrics=\"pymol_selection,sequence,ss,rosetta_sele\" name=\"run_metrics1\" prefix=\"m1_\"/>\n\t\t<RunSimpleMetrics metrics=\"timing,ss\" name=\"run_metrics2\" prefix=\"m2_\"/>\n\t</MOVERS>\n\t<PROTOCOLS>\n\t\t<Add mover_name=\"run_metrics1\"/>\n\t\t<Add mover_name=\"min_mover\"/>\n\t\t<Add mover_name=\"run_metrics2\"/>\n\t</PROTOCOLS>\n</ROSETTASCRIPTS>\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.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\nprotocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings\nprotocols.jd2.parser.MoveMapFactoryLoader: Defined MoveMap named \"movemap_L1\"\nprotocols.minimization_packing.MinMover: Found set MoveMap factory. Using this to define MoveMap.\ncore.select.movemap.util: Found MoveMapFactory movemap_L1\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"min_mover\" of type MinMover\ncore.simple_metrics.util: Added simple metric SelectedResiduesPyMOLMetric.\ncore.simple_metrics.util: Added simple metric SequenceMetric.\ncore.simple_metrics.util: Added simple metric SecondaryStructureMetric.\ncore.simple_metrics.util: Added simple metric SelectedResiduesMetric.\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"run_metrics1\" of type RunSimpleMetrics\ncore.simple_metrics.util: Added simple metric TimingProfileMetric.\ncore.simple_metrics.util: Added simple metric SecondaryStructureMetric.\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"run_metrics2\" of type RunSimpleMetrics\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"run_metrics1\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"min_mover\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"run_metrics2\"\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<SCOREFXNS/>\n\t<RESIDUE_SELECTORS>\n\t\t<CDR cdrs=\"L1\" name=\"L1\"/>\n\t</RESIDUE_SELECTORS>\n\t<MOVE_MAP_FACTORIES>\n\t\t<MoveMapFactory bb=\"0\" chi=\"0\" name=\"movemap_L1\">\n\t\t\t<Backbone residue_selector=\"L1\"/>\n\t\t\t<Chi residue_selector=\"L1\"/>\n\t\t</MoveMapFactory>\n\t</MOVE_MAP_FACTORIES>\n\t<SIMPLE_METRICS>\n\t\t<TimingProfileMetric name=\"timing\"/>\n\t\t<SelectedResiduesMetric name=\"rosetta_sele\" residue_selector=\"L1\" rosetta_numbering=\"1\"/>\n\t\t<SelectedResiduesPyMOLMetric name=\"pymol_selection\" residue_selector=\"L1\"/>\n\t\t<SequenceMetric name=\"sequence\" residue_selector=\"L1\"/>\n\t\t<SecondaryStructureMetric name=\"ss\" residue_selector=\"L1\"/>\n\t</SIMPLE_METRICS>\n\t<MOVERS>\n\t\t<MinMover movemap_factory=\"movemap_L1\" name=\"min_mover\" tolerance=\".1\"/>\n\t\t<RunSimpleMetrics metrics=\"pymol_selection,sequence,ss,rosetta_sele\" name=\"run_metrics1\" prefix=\"m1_\"/>\n\t\t<RunSimpleMetrics metrics=\"timing,ss\" name=\"run_metrics2\" prefix=\"m2_\"/>\n\t</MOVERS>\n\t<PROTOCOLS>\n\t\t<Add mover_name=\"run_metrics1\"/>\n\t\t<Add mover_name=\"min_mover\"/>\n\t\t<Add mover_name=\"run_metrics2\"/>\n\t</PROTOCOLS>\n</ROSETTASCRIPTS>\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings\nprotocols.jd2.parser.MoveMapFactoryLoader: Defined MoveMap named \"movemap_L1\"\nprotocols.minimization_packing.MinMover: Found set MoveMap factory. Using this to define MoveMap.\ncore.select.movemap.util: Found MoveMapFactory movemap_L1\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"min_mover\" of type MinMover\ncore.simple_metrics.util: Added simple metric SelectedResiduesPyMOLMetric.\ncore.simple_metrics.util: Added simple metric SequenceMetric.\ncore.simple_metrics.util: Added simple metric SecondaryStructureMetric.\ncore.simple_metrics.util: Added simple metric SelectedResiduesMetric.\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"run_metrics1\" of type RunSimpleMetrics\ncore.simple_metrics.util: Added simple metric TimingProfileMetric.\ncore.simple_metrics.util: Added simple metric SecondaryStructureMetric.\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"run_metrics2\" of type RunSimpleMetrics\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"run_metrics1\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"min_mover\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"run_metrics2\"\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: SRWGGDGFYAMDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<RESIDUE_SELECTORS>\n\t\t<CDR cdrs=\"L1\" name=\"L1\"/>\n\t</RESIDUE_SELECTORS>\n\t<PROTOCOLS/>\n</ROSETTASCRIPTS>\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings\nprotocols.rosetta_scripts.ParsedProtocol: ParsPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nL1 Residue: 24 L : 892\nL1 Residue: 25 L : 893\nL1 Residue: 26 L : 894\nL1 Residue: 27 L : 895\nL1 Residue: 28 L : 896\nL1 Residue: 29 L : 897\nL1 Residue: 38 L : 898\nL1 Residue: 39 L : 899\nL1 Residue: 40 L : 900\nL1 Residue: 41 L : 901\nL1 Residue: 42 L : 902\nL1 Residue: 24 L : 892\nL1 Residue: 25 L : 893\nL1 Residue: 26 L : 894\nL1 Residue: 27 L : 895\nL1 Residue: 28 L : 896\nL1 Residue: 29 L : 897\nL1 Residue: 38 L : 898\nL1 Residue: 39 L : 899\nL1 Residue: 40 L : 900\nL1 Residue: 41 L : 901\nL1 Residue: 42 L : 902\nedProtocol mover with the following settings\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: SRWGGDGFYAMDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\n[NbConvertApp] Converting notebook 02.07-RosettaScripts-in-PyRosetta.ipynb to python\n[NbConvertApp] Writing 11030 bytes to 02.07-RosettaScripts-in-PyRosetta.py\n/bin/sh: 1: pip: not found\n02.07-RosettaScripts-in-PyRosetta.py:119: 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.rosetta_scripts import *\n", "state": "passed"}, "02.08-Visualization-and-pyrosetta.distributed.viewer": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 02.08-Visualization-and-pyrosetta.distributed.viewer.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1779282845 seed_offset=0 real_seed=-1779282845\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1779282845 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.95654 seconds.\ncore.import_pose.import_pose: File 'inputs/3EK4.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'CRO' from the PDB components dictionary for residue type 'pdb_CRO'\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue pdb_CRO 164\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue VAL 165. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 165 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 349\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 163 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 165 with connection point 1\ncore.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 23 atom name OXT\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.dunbracPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\nHelp on function init in module pyrosetta.distributed.viewer.core:\n\ninit(packed_and_poses_and_pdbs=None, window_size=None, modules=None, delay=None, continuous_update=None, *args, **kwargs)\n Initialize the Viewer object.\n \n Parameters\n ----------\n first : required\n `packed_and_poses_and_pdbs`\n \n `PackedPose`, `Pose`, or `str` of a valid path to a .pdb file, or a `list`, `set`, or `tuple` of these objects.\n \n second : optional\n `window_size`\n \n `list` or `tuple` of `int` or `float` values for the (width, height) dimensions of the displayed window screen size.\n Default: (1200, 800)\n \n third : optional\n `modules`\n \n `list` of instantiated visualization modules to run upon changing amongst `packed_and_poses_and_pdbs` objects\n with the slider, matching the namespace `pyrosetta.distributed.viewer.set*`\n Default: []\n \n fourth : optional\n `delay`\n \n `float` or `int` time delay in seconds before rendering the Viewer in a Jupyter notebook, which is useful to prevent\n overburdening the Jupyter notebook client if `for` looping over quick modifications to a `Pose`, and should be >= 0.\n Default: 0.25\n \n fifth : optional\n `continuous_update`\n \n `True` or `False`. When using the interactive slider widget, `False` restricts rendering to mouse release events.\n Default: False\n \n Returns\n -------\n A Viewer instance.\n\nHelp on function coreBoundarySurface in module pyrosetta.distributed.viewer.presets:\n\ncoreBoundarySurface(packed_and_poses_and_pdbs=None, *args, **kwargs)\n Display core residues as 'blackCarbon' sticks, boundary residues as 'greyCarbon' sticks, and surface residues\n as 'whiteCarbon' sticks, with 'spectrum' cartoon representation, using the default arguments in\n `pyrosetta.rosetta.core.select.residue_selector.LayerSelector()` to select layers.\n \n @klimaj\n\nHelp on function ligandsAndMetals in module pyrosetta.distributed.viewer.presets:\n\nligandsAndMetals(packed_and_poses_and_pdbs=None, *args, **kwargs)\n Display residues with `ResidueProperty.LIGAND` as 'brownCarbon' sticks with opaque surface,\n and `ResidueProperty.METAL` as 'chainHetatm' spheres, with 'spectrum' cartoon representation,\n disulfide bonds, polar hydrogens, and dashed hydrogen bonds.\n \n @klimaj\n\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\rinteractive(children=(IntSlider(value=0, description='Decoys', max=8), Output()), _dom_classes=('widget-intera\u2026\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\rk.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.327235 seconds to load from binary\ncore.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_CRO:MP-N1-connect:MP-C3-connect\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File 'inputs/6MSR.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1 in file inputs/6MSR.pdb. Best match rsd_type: GLY:NtermProteinFull\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 134 in file inputs/6MSR.pdb. Best match rsd_type: GLY:NtermProteinFull\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 257 in file inputs/6MSR.pdb. Best match rsd_type: GLY:NtermProteinFull\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 32\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 32\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 32\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 83\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: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 102\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 106\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 109\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 109\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 109\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 111\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 111\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 112\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 112\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 152\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 152\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 152\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 160\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 160\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 160\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 166\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 166\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 182\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 187\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 187\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 187\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 189\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 189\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 189\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 228\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 228\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 228\ncore.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 8 atom name NE \ncore.pack.pack_missing_sidechains: packing residue \u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r\u001b[2K\rnumber 21 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 22 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 32 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 33 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 35 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 36 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 48 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 10 atom name NZ \ncore.pack.pack_missing_sidechains: packing residue number 83 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 9 atom name NZ \ncore.pack.pack_missing_sidechains: packing residue number 97 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 98 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 6 atom name OG \ncore.pack.pack_missing_sidechains: packing residue number 106 because of missing atom number 6 atom name OG \ncore.pack.pack_missing_sidechains: packing residue number 108 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 8 atom name CE \ncore.pack.pack_missing_sidechains: packing residue number 112 because of missing atom number 8 atom name CE \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 152 because of missing atom number 8 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 159 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 160 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 166 because of missing atom number 8 atom name CE \ncore.pack.pack_missing_sidechains: packing residue number 174 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 180 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 182 because of missing atom number 6 atom name OG \ncore.pack.pack_missing_sidechains: packing residue number 184 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 185 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 187 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 188 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 189 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 228 because of missing atom number 8 atom name CD \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 1014 rotamers at 35 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File 'inputs/1QCQ.pdb' automatically determined to be of type PDB\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHLLLLLEEEEEELLEEEEEEEEEEELLLLLLELLEEEEEEELLLLLLLLLL\u001b[2K\r<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\rEEEELLLLLELLELLLLEELLHHHLLLLLLLLLHHHHHHHHHHHHHLLLLLLLLLHHHHHHHHHLHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHLLLLLEEEEEELLEEEEEEEEEEELLLLLLELLEEEEEEELLLLLLLLLLEEEELLLLLELLELLLLEELLHHHLLLLLLLLLHHHHHHHHHHHHHLLLLLLLLLHHHHHHHHHLHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHLLLLLEEEEEELLEEEEEEEEEEELLLLLLELLEEEEEEELLLLLLLLLLEEEELLLLLELLELLLLEELLHHHLLLLLLLLLHHHHHHHHHHHHHLLLLLLLLLHHHHHHHHHLHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHLLLLLEEEEEELLEEEEEEEEEEELLLLLLELLEEEEEEELLLLLLLLLLEEEELLLLLELLELLLLEELLHHHLLLLLLLLLHHHHHHHHHHHHHLLLLLLLLLHHHHHHHHHLHHHHHHHHHHHHHHHLL\ncore.import_pose.import_pose: File 'inputs/2FD7.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 15\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 15\ncore.conformation.Conformation: Found disulfide between residues 3 40\ncore.conformation.Conformation: current variant for 3 CYS\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 3 CYD\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: Found disulfide between residues 4 32\ncore.conformation.Conformation: current variant for 4 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 4 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 16 26\ncore.conformation.Conformation: current variant for 16 CYS\ncore.conformation.Conformation: current variant for 26 CYS\ncore.conformation.Conformation: current variant for 16 CYD\ncore.conformation.Conformation: current variant for 26 CYD\ncore.pack.pack_missing_sidechains: packing residue number 15 because of missing atom number 6 atom name CG1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.mm.MMBondAngleLibrary: MM bond angle sets added fully assigned: 604; wildcard: 0 and 1 virtual parameter.\nbasic.io.database: Database file opened: sampling/branch_angle/branch_angle_1.txt\nbasic.io.database: Database file opened: sampling/branch_angle/branch_angle_2.txt\nprotocols.backrub.BackrubMover: Segment lengths: 3-34 atoms\nprotocols.backrub.BackrubMover: Main chain pivot atoms: CA\nprotocols.backrub.BackrubMover: Adding backrub segments for residues 1-46\nprotocols.backrub.BackrubMover: Total Segments Added: 346\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nbasic.io.database: Database file opened: protocol_data/crick_parameters/alpha_helix.crick_params\nbasic.io.database: Database file opened: protocol_data/crick_parameters/alpha_helix.crick_params\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\rMakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r\u001b[2K\r.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nbasic.io.database: Database file opened: protocol_data/crick_parameters/alpha_helix.crick_params\nbasic.io.database: Database file opened: protocol_data/crick_parameters/alpha_helix.crick_params\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equati\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\rons.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: \u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\rBuilding a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundle: Building a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick \u001b[2K\r\u001b[2K\requations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\nprotocols.helical_bundle.MakeBundleHelix: Building a helix in a helical bundle using the Crick equations.\ncore.import_pose.import_pose: File 'inputs/3EK4.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue pdb_CRO 164\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue VAL 165. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 165 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 349\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 163 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 165 with connection point 1\ncore.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 23 atom name OXT\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_CRO:MP-N1-connect:MP-C3-connect\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File 'inputs/6MSR.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1 in file inputs/6MSR.pdb. Best match rsd_type: GLY:NtermProteinFull\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 134 in file inputs/6MSR.pdb. Best match rsd_type: GLY:NtermProteinFull\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 257 in file inputs/6MSR.pdb. Best match rsd_type: GLY:NtermProteinFull\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 7\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 21\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 22\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 32\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 32\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 32\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 33\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 35\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 36\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 48\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 83\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 83\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: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 97\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 98\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 102\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 106\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 109\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 109\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 109\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 111\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 111\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 112\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 112\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 152\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 152\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 152\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 159\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 160\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 160\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 160\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 166\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 166\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 174\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 180\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 182\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 184\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 185\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 187\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 187\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 187\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 188\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 189\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 189\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 189\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 228\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 228\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 228\ncore.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 8 atom name NE \ncore.pack.pack_missing_sidechains: packing residue number 21 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 22 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 32 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 33 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 35 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 36 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 48 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 10 atom name NZ \ncore.pack.pack_missing_sidechains: packing residue number 83 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 9 atom name NZ \ncore.pack.pack_missing_sidechains: packing residue number 97 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 98 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 6 atom name OG \ncore.pack.pack_missing_sidechains: packing residue number 106 because of missing atom number 6 atom name OG \ncore.pack.pack_missing_sidechains: packing residue number 108 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 8 atom name CE \ncore.pack.pack_missing_sidechains: packing residue number 112 because of missing atom number 8 atom name CE \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 152 because of missing atom number 8 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 159 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 160 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 166 because of missing atom number 8 atom name CE \ncore.pack.pack_missing_sidechains: packing residue number 174 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 180 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 182 because of missing atom number 6 atom name OG \ncore.pack.pack_missing_sidechains: packing residue number 184 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 185 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 187 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 188 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 189 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 228 because of missing atom number 8 atom name CD \ncore.pack.task: Packer task: initialize from command line() \ncore.s\u001b[2K\r<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\rinteractive(children=(IntSlider(value=0, description='Decoys', max=3), Output()), _dom_classes=('widget-intera\u2026\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\r\u001b[2K\r\u001b[2K\rinteractive(children=(IntSlider(value=0, continuous_update=False, description='Decoys', max=3), Output()), _do\u2026\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\rHelp on class setBackgroundColor in module pyrosetta.distributed.viewer.modules:\n\nclass setBackgroundColor(builtins.object)\n | setBackgroundColor(color=4294967295)\n | \n | Set Viewer background color with either Hexcode or standard colors.\n | \n | Parameters\n | ----------\n | first : optional\n | `color`\n | \n | Hexcode literal (e.g. 0xffffffff) or `str` indicating a standard color (e.g. \"black\").\n | Default: 0xffffffff\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, color=4294967295)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setDisulfides in module pyrosetta.distributed.viewer.modules:\n\nclass setDisulfides(builtins.object)\n | setDisulfides(color='gold', radius=0.5)\n | \n | Display disulfide bonds according to `pyrosetta.rosetta.core.conformation.is_disulfide_bond()`\n | for all combinations of cysteine residues in each initialized `.pdb` file, `Pose` or `PackedPose` object.\n | \n | Parameters\n | ----------\n | first : optional\n | `color`\n | \n | `str` indicating a standard color (e.g. \"black\").\n | Default: \"gold\"\n | \n | second : optional\n | `radius`\n | \n | `float` or `int` indicating the radius of the stick connecting the atoms participating in each disulfide bond.\n | Default: 0.5\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, color='gold', radius=0.5)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setHydrogenBonds in module pyrosetta.distributed.viewer.modules:\n\nclass setHydrogenBonds(builtins.object)\n | setHydrogenBonds(color='black', dashed=True, radius=None)\n | \n | Display hydrogen bonds according to `pyrosetta.rosetta.core.pose.Pose.get_hbonds()`\n | in each initialized `.pdb` file, `Pose` or `PackedPose` object.\n | \n | Parameters\n | ----------\n | first : optional\n | `color`\n | \n | `str` indicating a standard color (e.g. \"yellow\").\n | Default: \"black\"\n | \n | second : optional\n | `dashed`\n | \n | `True` or `False` to show hydrogen bonds as dashed lines.\n | If `True`, then option `radius` must be `None`.\n | If `False`, then option `radius` must be specified.\n | Default: True\n | \n | third : optional\n | `radius`\n | \n | `float` or `int` indicating the radius of the solid (non-dashed) stick connecting the atoms participating\n | in each hydrogen bond. If set, this automatically sets the option `dashed` to `False`.\n | Default: None\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, color='black', dashed=True, radius=None)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setHydrogens in module pyrosetta.distributed.viewer.modules:\n\nclass setHydrogens(builtins.object)\n | setHydrogens(color='white', radius=0.05, polar_only=False)\n | \n | Show all or only polar hydrogen atoms in each initialized `.pdb` file, `Pose` or `PackedPose` object.\n | \n | Parameters\n | ----------\n | first : optional\n | `color`\n | \n | `str` indicating a standard color (e.g. \"grey\").\n | Default: \"white\"\n | \n | second : optional\n | `radius`\n | \n | `float` or `int` indicating the radius of the hydrogen atom stick represnetations.\n | Default: 0.05\n | \n | third : optional\n | `polar_only`\n | \n | `True` or `False`. `True` to show only polar hydrogen atoms, and `False` to show all hydrogen atoms.\n | Default: False\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, color='white', radius=0.05, polar_only=False)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setStyle in module pyrosetta.distributed.viewer.modules:\n\nclass setStyle(builtins.object)\n | setStyle(residue_selector=None, cartoon=True, cartoon_color='spectrum', style='stick', colorscheme='blackCarbon', radius='0.1', label=True, label_fontsize=12, label_background=False, label_fontcolor='black', command=None)\n | \n | Show and color cartoon, and/or show heavy atoms with provided style, color and radius for each initialized\n | `.pdb` file, `Pose` or `PackedPose` object. If the `residue_selector` argument is provided, apply styles\n | only to the selected residues. If the `command` argument is provided, override all other arguments and pass\n | `py3Dmol.view.setStyle()` commands to the Viewer.\n | \n | Parameters\n | ----------\n | first : optional\n | `residue_selector`\n | \n | An instance of `pyrosetta.rosetta.core.select.residue_selector.ResidueSelector` on which to apply the style(s).\n | Default: None\n | \n | second : optional\n | `cartoon`\n | \n | `True` or `False` to show cartoon representation.\n | Default: True\n | \n | third : optional\n | `cartoon_color`\n | \n | Hexcode literal (e.g. 0xAF10AB) or `str` indicating a standard color (e.g. \"grey\") for the cartoon representation.\n | If \"spectrum\", apply reversed color gradient based on residue numbers. The option `cartoon` must also be set to `True`.\n | Default: \"spectrum\"\n | Reference: https://3dmol.csb.pitt.edu/doc/types.html#ColorSpec\n | \n | fourth : optional\n | `style`\n | \n | `str` indicating a representation style of heavy atoms, choosing from either \"line\", \"cross\", \"stick\", or \"sphere\".\n | Default: \"stick\"\n | \n | fifth : optional\n | `colorscheme`\n | \n | `str` indicating the color scheme for heavy atoms represented by the `style` option. Options include:\n | A lower-case standard color followed by \"Carbon\" (e.g. \"orangeCarbon\")\n | \"ssPyMOL\": PyMol secondary colorscheme\n | \"ssJmol\": Jmol secondary colorscheme\n | \"Jmol\": Jmol primary colorscheme\n | \"default\": default colorscheme\n | \"amino\": amino acid colorscheme\n | \"shapely\": shapely protien colorscheme\n | \"nucleic\": nucleic acid colorscheme\n | \"chain\": standard chain colorscheme\n | \"chainHetatm\": chain Hetatm colorscheme\n | Default: \"blackCarbon\"\n | Reference: https://3dmol.csb.pitt.edu/doc/types.html#ColorschemeSpec\n | \n | sixth : optional\n | `radius`\n | \n | `float` or `int` indicating the radius of the heavy atoms represented by the `style` option.\n | Default: 0.1\n | \n | seventh : optional\n | `label`\n | \n | `True` or `False` to show labels next to residues selected by the `residue_selector` option. \n | Default: True\n | \n | eighth : optional\n | `label_fontsize`\n | \n | `int` or `float` indicating the font size of labels next to residues selected by the `residue_selector` option,\n | only if `label` is `True`.\n | Default: 12\n | \n | ninth : optional\n | `label_background`\n | \n | `True` or `False` to show the background of labels next to residues selected by the `residue_selector` option,\n | only if `label` is `True`.\n | Default: False\n | \n | tenth : optional\n | `label_fontcolor`\n | \n | `str` indicating a standard font color (e.g. \"grey\") for label text next to residues selected by the `residue_selector` option,\n | only if `label` is `True`.\n | Default: \"black\"\n | \n | eleventh : optional\n | `command`\n | \n | `dict` or `tuple` of `dict`s of `py3Dmol.view.setStyle()` commands. If specified, this option overrides all other options.\n | Default: None\n | Example:\n | command = {\"hetflag\": True}, {\"stick\": {\"singleBond\": False, \"colorscheme\": \"greyCarbon\", \"radius\": 0.15}}\n | view = viewer.init(poses) + viewer.setStyle(command=command)\n | view.show()\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, residue_selector=None, cartoon=True, cartoon_color='spectrum', style='stick', colorscheme='blackCarbon', radius='0.1', label=True, label_fontsize=12, label_background=False, label_fontcolor='black', command=None)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setSurface in module pyrosetta.distributed.viewer.modules:\n\nclass setSurface(builtins.object)\n | setSurface(residue_selector=None, surface_type='VDW', opacity=0.5, color=None, colorscheme=None)\n | \n | Show the specified surface for each initialized `.pdb` file, `Pose` or `PackedPose` object.\n | \n | Parameters\n | ----------\n | first : optional\n | `residue_selector`\n | \n | An instance of `pyrosetta.rosetta.core.select.residue_selector.ResidueSelector` to select residues\n | on which to apply the surface.\n | Default: None\n | \n | second : optional\n | `surface_type`\n | \n | `str` indicating surface type to be displayed. py3Dmol supports the following options:\n | \"VDW\": Van der Waals surface\n | \"MS\": Molecular surface\n | \"SES\": Solvent excluded surface\n | \"SAS\": Solvent accessible surface\n | Default: \"VDW\"\n | \n | third : optional\n | `opacity`\n | \n | `float` or `int` between 0 and 1 for opacity of the displayed surface.\n | Default: 0.5\n | \n | fourth : optional\n | `color`\n | \n | `str` indicating a standard color (e.g. \"grey\") of the surface to be displayed. \n | Either `color` or `colorscheme` may be specified, where `colorscheme` overrides `color`.\n | Default: None\n | \n | fifth : optional\n | `colorscheme`\n | \n | `str` indicating the color scheme of the surface to be displayed.\n | Either `color` or `colorscheme` may be specified, where `colorscheme` overrides `color`.\n | Options include:\n | A lower-case standard color followed by \"Carbon\" (e.g. \"yellowCarbon\")\n | \"ssPyMOL\": PyMol secondary colorscheme\n | \"ssJmol\": Jmol secondary colorscheme\n | \"Jmol\": Jmol primary colorscheme\n | \"default\": default colorscheme\n | \"amino\": amino acid colorscheme\n | \"shapely\": shapely protien colorscheme\n | \"nucleic\": nucleic acid colorscheme\n | \"chain\": standard chain colorscheme\n | \"chainHetatm\": chain Hetatm colorscheme\n | Default: None\n | Reference: https://3dmol.csb.pitt.edu/doc/types.html#ColorschemeSpec\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, residue_selector=None, surface_type='VDW', opacity=0.5, color=None, colorscheme=None)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setZoom in module pyrosetta.distributed.viewer.modules:\n\nclass setZoom(builtins.object)\n | setZoom(factor=2)\n | \n | Set the zoom magnification factor of each initialized `.pdb` file, `Pose` or `PackedPose` object.\n | Values >1 zoom in, and values <1 zoom out.\n | \n | Parameters\n | ----------\n | first : optional\n | `factor`\n | \n | `float` or `int` indicating the zoom magnification factor.\n | Default: 2\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, factor=2)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\nHelp on class setZoomTo in module pyrosetta.distributed.viewer.modules:\n\nclass setZoomTo(builtins.object)\n | setZoomTo(residue_selector=None)\n | \n | Zoom to a `ResidueSelector` in each initialized `.pdb` file, `Pose` or `PackedPose` object.\n | \n | Parameters\n | ----------\n | first : optional\n | `residue_selector`\n | \n | An instance of `pyrosetta.rosetta.core.select.residue_selector.ResidueSelector` into which to zoom.\n | Default: None\n | \n | Returns\n | -------\n | A Viewer instance.\n | \n | Methods defined here:\n | \n | __init__(self, residue_selector=None)\n | Initialize self. See help(type(self)) for accurate signature.\n | \n | apply(self, viewer, pose, pdbstring)\n | \n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n | \n | __dict__\n | dictionary for instance variables (if defined)\n | \n | __weakref__\n | list of weak references to the object (if defined)\n\ncoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 1014 rotamers at 35 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File 'inputs/1QCQ.pdb' automatically determined to be of type PDB\ncore.import_pose.import_pose: File 'inputs/2FD7.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 15\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 15\ncore.conformation.Conformation: Found disulfide between residues 3 40\ncore.conformation.Conformation: current variant for 3 CYS\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 3 CYD\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: Found disulfide between residues 4 32\ncore.conformation.Conformation: current variant for 4 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 4 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 16 26\ncore.conformation.Conformation: current variant for 16 CYS\ncore.conformation.Conformation: current variant for 26 CYS\ncore.conformation.Conformation: current variant for 16 CYD\ncore.conformation.Conformation: current variant for 26 CYD\ncore.pack.pack_missing_sidechains: packing residue number 15 because of missing atom number 6 atom name CG1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting core=true boundary=false surface=false in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting core=false boundary=true surface=false in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting core=false boundary=false surface=true in LayerSelector.\n[NbConvertApp] Converting notebook 02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb to python\n[NbConvertApp] Writing 16297 bytes to 02.08-Visualization-and-pyrosetta.distributed.viewer.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "03.00-Rosetta-Energy-Score-Functions": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 03.00-Rosetta-Energy-Score-Functions.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 03.00-Rosetta-Energy-Score-Functions.py\n[NbConvertApp] Converting notebook 03.00-Rosetta-Energy-Score-Functions.ipynb to python\n[NbConvertApp] Writing 2469 bytes to 03.00-Rosetta-Energy-Score-Functions.py\n", "state": "passed"}, "03.01-Score-Function-Basics": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 03.01-Score-Function-Basics.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 03.01-Score-Function-Basics.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-317286382 seed_offset=0 real_seed=-317286382\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-317286382 RG_type=mt19937\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\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\n1215.7290700424core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=379459796 seed_offset=0 real_seed=379459796\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=379459796 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.78469 seconds.\ncore.import_pose.import_pose: File 'inputs/6Q21_A.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.352975 seconds to load from binary\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr \n154.59159174026854\nNone\n 1.000 -1039.246 -1039.246\n fa_rep 0.550 1193.837 656.611\n fa_sol 1.000 682.582 682.582\n fa_intra_rep 0.005 700.419 3.502\n fa_intra_sol_xover4 1.000 46.564 46.564\n lk_ball_wtd 1.000 -14.597 -14.597\n fa_elec 1.000 -195.387 -195.387\n pro_close 1.250 97.210 121.513\n hbond_sr_bb 1.000 -41.656 -41.656\n hbond_lr_bb 1.000 -28.352 -28.352\n hbond_bb_sc 1.000 -13.111 -13.111\n hbond_sc 1.000 -7.771 -7.771\n dslf_fa13 1.250 0.000 0.000\n omega 0.400 41.525 16.610\n fa_dun 0.700 1296.642 907.650\n p_aa_pp 0.600 -25.496 -15.298\n yhh_planarity 0.625 0.000 0.000\n ref 1.000 47.114 47.114\n rama_prepro 0.450 197.781 89.002\n---------------------------------------------------\n Total weighted score: 1215.729\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\n[NbConvertApp] Converting notebook 03.01-Score-Function-Basics.ipynb to python\n[NbConvertApp] Writing 8023 bytes to 03.01-Score-Function-Basics.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "03.02-Analyzing-energy-between-residues": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 03.02-Analyzing-energy-between-residues.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 03.02-Analyzing-energy-between-residues.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-435511804 seed_offset=0 real_seed=-435511804\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-435511804 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=477076618 seed_offset=0 real_seed=477076618\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=477076618 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 1.82635 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.import_pose.import_pose: File '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: current variant for 6 CYS\ncore.conformation.Conformation: current variant for 33 CYS\ncore.conformation.Conformation: current variant for 6 CYD\ncore.conformation.Conformation: current variant for 33 CYD\ncore.conformation.Conformation: Found disulfide between residues 132 162\ncore.conformation.Conformation: current variant for 132 CYS\ncore.conformation.Conformation: current variant for 162 CYS\ncore.conformation.Conformation: current variant for 132 CYD\ncore.conformation.Conformation: current variant for 162 CYD\ncore.conformation.Conformation: Found disulfide between residues 165 174\ncore.conformation.Conformation: current variant for 165 CYS\ncore.conformation.Conformation: current variant for 174 CYS\ncore.conformation.Conformation: current variant for 165 CYD\ncore.conformation.Conformation: current variant for 174 CYD\ncore.conformation.Conformation: Found disulfide between residues 169 182\ncore.conformation.Conformation: current variant for 169 CYS\ncore.conformation.Conformation: current variant for 182 CYS\ncore.conformation.Conformation: current variant for 169 CYD\ncore.conformation.Conformation: current variant for 182 CYD\ncore.conformation.Conformation: Found disulfide between residues 190 198\ncore.conformation.Conformation: current variant for 190 CYS\ncore.conformation.Conformation: current variant for 198 CYS\ncore.conformation.Conformation: current variant for 190 CYD\ncore.conformation.Conformation: current variant for 198 CYD\ncore.conformation.Conformation: Found disulfide between residues 194 206\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 206 CYS\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: current variant for 206 CYD\ncore.conformation.Conformation: Found disulfide between residues 207 215\ncore.conformation.Conformation: current variant for 207 CYS\ncore.conformation.Conformation: current variant for 215 CYS\ncore.conformation.Conformation: current variant for 207 CYD\ncore.conformation.Conformation: current variant for 215 CYD\ncore.conformation.Conformation: Found disulfide between residues 211 223\ncore.conformation.Conformation: current variant for 211 CYS\ncore.conformation.Conformation: current variant for 223 CYS\ncore.conformation.Conformation: current variant for 211 CYD\ncore.conformation.Conformation: current variant for 223 CYD\ncore.conformation.Conformation: Found disulfide between residues 226 235\ncore.conformation.Conformation: current variant for 226 CYS\ncore.conformation.Conformation: current variant for 235 CYS\ncore.conformation.Conformation: current variant for 226 CYD\ncore.conformation.Conformation: current variant for 235 CYD\ncore.conformation.Conformation: Found disulfide between residues 239 266\ncore.conformation.Conformation: current variant for 239 CYS\ncore.conformation.Conformation: current variant for 266 CYS\ncore.conformation.Conformation: current variant for 239 CYD\ncore.conformation.Conformation: current variant for 266 CYD\ncore.conformation.Conformation: Found disulfide between residues 270 282\ncore.conformation.Conformation: current variant for 270 CYS\ncore.conformation.Conformation: current variant for 282 CYS\ncore.conformation.Conformation: current variant for 270 CYD\ncore.conformation.Conformation: current variant for 282 CYD\ncore.conformation.Conformation: Found disulfide between residues 286 301\ncore.conformation.Conformation: current variant for 286 CYS\ncore.conformation.Conformation: current variant for 301 CYS\ncore.conformation.Conformation: current variant for 286 CYD\ncore.conformation.Conformation: current variant for 301 CYD\ncore.conformation.Conformation: Found disulfide between residues 304 308\ncore.conformation.Conformation: current variant for 304 CYS\ncore.conformation.Conformation: current variant for 308 CYS\ncore.conformation.Conformation: current variant for 304 CYD\ncore.conformation.Conformation: current variant for 308 CYD\ncore.conformation.Conformation: Found disulfide between residues 312 337\ncore.conformation.Conformation: current variant for 312 CYS\ncore.conformation.Conformation: current variant for 337 CYS\ncore.conformation.Conformation: current variant for 312 CYD\ncore.conformation.Conformation: current variant for 337 CYD\ncore.conformation.Conformation: Found disulfide between residues 445 474\ncore.conformation.Conformation: current variant for 445 CYS\ncore.conformation.Conformation: current variant for 474 CYS\ncore.conformation.Conformation: current variant for 445 CYD\ncore.conformation.Conformation: current variant for 474 CYD\ncore.conformation.Conformation: Found disulfide between residues 481 490\ncore.conformation.Conformation: current variant for 481 CYS\ncore.conformation.Conformation: current variant for 490 CYS\ncore.conformation.Conformation: current variant for 481 CYD\ncore.conformation.Conformation: current variant for 490 CYD\ncore.conformation.Conformation: Found disulfide between residues 485 498\ncore.conformation.Conformation: current variant for 485 CYS\ncore.conformation.Conformation: current variant for 498 CYS\ncore.conformation.Conformation: current variant for 485 CYD\ncore.conformation.Conformation: current variant for 498 CYD\ncore.conformation.Conformation: Found disulfide between residues 501 510\ncore.conformation.Conformation: current variant for 501 CYS\ncore.conformation.Conformation: current variant for 510 CYS\ncore.conformation.Conformation: current variant for 501 CYD\ncore.conformation.Conformation: current variant for 510 CYD\ncore.conformation.Conformation: Found disulfide between residues 514 530\ncore.conformation.Conformation: current variant for 514 CYS\ncore.conformation.Conformation: current variant for 530 CYS\ncore.conformation.Conformation: current variant for 514 CYD\ncore.conformation.Conformation: current variant for 530 CYD\ncore.conformation.Conformation: Found disulfide between residues 533 546\ncore.conformation.Conformation: current variant for 533 CYS\ncore.conformation.Conformation: current variant for 546 CYS\ncore.conformation.Conformation: current variant for 533 CYD\ncore.conformation.Conformation: current variant for 546 CYD\ncore.conformation.Conformation: Found disulfide between residues 537 554\ncore.conformation.Conformation: current variant for 537 CYS\ncore.conformation.Conformation: current variant for 554 CYS\ncore.conformation.Conformation: current variant for 537 CYD\ncore.conformation.Conformation: current variant for 554 CYD\ncore.conformation.Conformation: Found disulfide between residues 557 566\ncore.conformation.Conformation: current variant for 557 CYS\ncore.conformation.Conformation: current variant for 566 CYS\ncore.conformation.Conformation: current variant for 557 CYD\ncore.conformation.Conformation: current variant for 566 CYD\ncore.conformation.Conformation: Found disulfide between residues 570 592\ncore.conformation.Conformation: current variant for 570 CYS\ncore.conformation.Conformation: current variant for 592 CYS\ncore.conformation.Conformation: current variant for 570 CYD\ncore.conformation.Conformation: current variant for 592 CYD\ncore.conformation.Conformation: Found disulfide between residues 595 603\ncore.conformation.Conformation: current variant for 595 CYS\ncore.conformation.Conformation: current variant for 603 CYS\ncore.conformation.Conformation: current variant for 595 CYD\ncore.conformation.Conformation: current variant for 603 CYD\ncore.conformation.Conformation: Found disulfide between residues 599 611\ncore.conformation.Conformation: current variant for 599 CYS\ncore.conformation.Conformation: current variant for 611 CYS\ncore.conformation.Conformation: current variant for 599 CYD\ncore.conformation.Conformation: current variant for 611 CYD\ncore.conformation.Conformation: Found disulfide between residues 636 701\ncore.conformation.Conformation: current variant for 636 CYS\ncore.conformation.Conformation: current variant for 701 CYS\ncore.conformation.Conformation: current variant for 636 CYD\ncore.conformation.Conformation: current variant for 701 CYD\ncore.conformation.Conformation: Found disulfide between residues 747 807\ncore.conformation.Conformation: current variant for 747 CYS\ncore.conformation.Conformation: current variant for 807 CYS\ncore.conformation.Conformation: current variant for 747 CYD\ncore.conformation.Conformation: current variant for 807 CYD\ncore.conformation.Conformation: Found disulfide between residues 846 919\ncore.conformation.Conformation: current variant for 846 CYS\ncore.conformation.Conformation: current variant for 919 CYS\ncore.conformation.Conformation: current variant for 846 CYD\ncore.conformation.Conformation: current variant for 919 CYD\ncore.conformation.Conformation: Found disulfide between residues 970 1026\ncore.conformation.Conformation: current variant for 970 CYS\ncore.conformation.Conformation: current variant for 1026 CYS\ncore.conformation.Conformation: current variant for 970 CYD\ncore.conformation.Conformation: current variant for 1026 CYD\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\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_PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n-1.2098840439684349\n0.10835353848860374\n1.5729435146961963\nlib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.357034 seconds to load from binary\ncore.pack.pack_rotamers: built 313 rotamers at 23 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 03.02-Analyzing-energy-between-residues.ipynb to python\n[NbConvertApp] Writing 3714 bytes to 03.02-Analyzing-energy-between-residues.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "03.03-Energies-and-the-PyMOLMover": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 03.03-Energies-and-the-PyMOLMover.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 03.03-Energies-and-the-PyMOLMover.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=926694423 seed_offset=0 real_seed=926694423\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=926694423 RG_type=mt19937\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1874325959 seed_offset=0 real_seed=1874325959\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1874325959 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.72504 seconds.\ncore.import_pose.import_pose: File 'inputs/6Q21_A.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.359222 seconds to load from binary\n[NbConvertApp] Converting notebook 03.03-Energies-and-the-PyMOLMover.ipynb to python\n[NbConvertApp] Writing 4360 bytes to 03.03-Energies-and-the-PyMOLMover.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "04.00-Introduction-to-Folding": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 04.00-Introduction-to-Folding.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 04.00-Introduction-to-Folding.py\n[NbConvertApp] Converting notebook 04.00-Introduction-to-Folding.ipynb to python\n[NbConvertApp] Writing 2766 bytes to 04.00-Introduction-to-Folding.py\n", "state": "passed"}, "04.01-Basic-Folding-Algorithm": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 04.01-Basic-Folding-Algorithm.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 04.01-Basic-Folding-Algorithm.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1580982769 seed_offset=0 real_seed=1580982769\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1580982769 RG_type=mt19937\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nphi: 180\npsi: 180\nIteration # 0\nCurrent pose score: 29.967\nLowest pose score: 29.967\nIteration # 1\nCurrent pose score: 27.105\nLowest pose score: 27.105\nIteration # 2\nCurrent pose score: 27.105\nLowest pose score: 27.105\nIteration # 3\nCurrent pose score: 26.370\nLowest pose score: 26.370\nIteration # 4\nCurrent pose score: 24.605\nLowest pose score: 24.605\nIteration # 5\nCurrent pose score: 25.052\nLowest pose score: 24.605\nIteration # 6\nCurrent pose score: 25.052\nLowest pose score: 24.605\nIteration # 7\nCurrent pose score: 25.052\nLowest pose score: 24.605\nIteration # 8\nCurrent pose score: 25.052\nLowest pose score: 24.605\nIteration # 9\nCurrent pose score: 25.052\nLowest pose score: 24.605\nIteration # 10\nCurrent pose score: 24.485\nLowest pose score: 24.485\nIteration # 11\nCurrent pose score: 24.025\nLowest pose score: 24.025\nIteration # 12\nCurrent pose score: 24.025\nLowest pose score: 24.025\nIteration # 13\nCurrent pose score: 24.025\nLowest pose score: 24.025\nIteration # 14\nCurrent pose score: 23.579\nLowest pose score: 23.579\nIteration # 15\nCurrent pose score: 20.850\nLowest pose score: 20.850\nIteration # 16\nCurrent pose score: 20.850\nLowest pose score: 20.850\nIteration # 17\nCurrent pose score: 20.920\nLowest pose score: 20.850\nIteration # 18\nCurrent pose score: 20.920\nLowest pose score: 20.850\nIteration # 19\nCurrent pose score: 20.396\nLowest pose score: 20.396\nIteration # 20\nCurrent pose score: 20.396\nLowest pose score: 20.396\nIteration # 21\nCurrent pose score: 20.442\nLowest pose score: 20.396\nIteration # 22\nCurrent pose score: 20.442\nLowest pose score: 20.396\nIteration # 23\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 24\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 25\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 26\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 27\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 28\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 29\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 30\nCurrent pose score: 20.425\nLowest pose score: 20.396\nIteration # 31\nCurrent pose score: 19.899\nLowest pose score: 19.899\nIteration # 32\nCurrent pose score: 19.828\nLowest pose score: 19.828\nIteration # 33\nCurrent pose score: 17.434\nLowest pose score: 17.434\nIteration # 34\nCurrent pose score: 17.434\nLowest pose score: 17.434\nIteration # 35\nCurrent pose score: 17.643\nLowest pose score: 17.434\nIteration # 36\nCurrent pose score: 15.334\nLowest pose score: 15.334\nIteration # 37\nCurrent pose score: 15.334\nLowest pose score: 15.334\nIteration # 38\nCurrent pose score: 16.028\nLowest pose score: 15.334\nIteration # 39\nCurrent pose score: 16.028\nLowest pose score: 15.334\nIteration # 40\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 41\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 42\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 43\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 44\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 45\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 46\nCurrent pose score: 13.422\nLowest pose score: 13.422\nIteration # 47\nCurrent pose score: 12.982\nLowest pose score: 12.982\nIteration # 48\nCurrent pose score: 13.029\nLowest pose score: 12.982\nIteration # 49\nCurrent pose score: 13.029\nLowest pose score: 12.982\nIteration # 50\nCurrent pose score: 13.029\nLowest pose score: 12.982\nIteration # 51\nCurrent pose score: 10.564\nLowest pose score: 10.564\nIteration # 52\nCurrent pose score: 10.564\nLowest pose score: 10.564\nIteration # 53\nCurrent pose score: 10.564\nLowest pose score: 10.564\nIteration # 54\nCurrent pose score: 10.564\nLowest pose score: 10.564\nIteration # 55\nCurrent pose score: 10.318\nLowest pose score: 10.318\nIteration # 56\nCurrent pose score: 10.318\nLowest pose score: 10.318\nIteration # 57\nCurrent pose score: 10.318\nLowest pose score: 10.318\nIteration # 58\nCurrent pose score: 10.318\nLowest pose score: 10.318\nIteration # 59\nCurrent pose score: 8.594\nLowest pose score: 8.594\nIteration # 60\nCurrent pose score: 8.594\nLowest pose score: 8.594\nIteration # 61\nCurrent pose score: 9.448\nLowest pose score: 8.594\nIteration # 62\nCurrent pose score: 8.716\nLowest pose score: 8.594\nIteration # 63\nCurrent pose score: 8.716\nLowest pose score: 8.594\nIteration # 64\nCurrent pose score: 8.716\nLowest pose score: 8.594\nIteration # 65\nCurrent pose score: 8.602\nLowest pose score: 8.594\nIteration # 66\nCurrent pose score: 8.399\nLowest pose score: 8.399\nIteration # 67\nCurrent pose score: 8.399\nLowest pose score: 8.399\nIteration # 68\nCurrent pose score: 8.399\nLowest pose score: 8.399\nIteration # 69\nCurrent pose score: 8.399\nLowest pose score: 8.399\nIteration # 70\nCurrent pose score: 8.622\nLowest pose score: 8.399\nIteration # 71\nCurrent pose score: 8.622\nLowest pose score: 8.399\nIteration # 72\nCurrent pose score: 8.622\nLowest pose score: 8.399\nIteration # 73\nCurrent pose score: 8.984\nLowest pose score: 8.399\nIteration # 74\nCurrent pose score: 8.984\nLowest pose score: 8.399\nIteration # 75\nCurrent pose score: 8.984\nLowest pose score: 8.399\nIteration # 76\nCurrent pose score: 8.271\nLowest pose score: 8.271\nIteration # 77\nCurrent pose score: 8.425\nLowest pose score: 8.271\nIteration # 78\nCurrent pose score: 8.425\nLowest pose score: 8.271\nIteration # 79\nCurrent pose score: 8.219\nLowest pose score: 8.219\nIteration # 80\nCurrent pose score: 8.219\nLowest pose score: 8.219\nIteration # 81\nCurrent pose score: 8.219\nLowest pose score: 8.219\nIteration # 82\nCurrent pose score: 8.219\nLowest pose score: 8.219\nIteration # 83\nCurrent pose score: 8.666\nLowest pose score: 8.219\nIteration # 84\nCurrent pose score: 8.666\nLowest pose score: 8.219\nIteration # 85\nCurrent pose score: 8.761\nLowest pose score: 8.219\nIteration # 86\nCurrent pose score: 8.425\nLowest pose score: 8.219\nIteration # 87\nCurrent pose score: 9.243\nLowest pose score: 8.219\nIteration # 88\nCurrent pose score: 9.184\nLowest pose score: 8.219\nIteration # 89\nCurrent pose score: 9.873\nLowest pose score: 8.219\nIteration # 90\nCurrent pose score: 9.873\nLowest pose score: 8.219\nIteration # 91\nCurrent pose score: 9.873\nLowest pose score: 8.219\nIteration # 92\nCurrent pose score: 9.873\nLowest pose score: 8.219\nIteration # 93\nCurrent pose score: 9.007\nLowest pose score: 8.219\nIteration # 94\nCurrent pose score: 9.007\nLowest pose score: 8.219\nIteration # 95\nCurrent pose score: 9.905\nLowest pose score: 8.219\nIteration # 96\nCurrent pose score: 10.456\nLowest pose score: 8.219\nIteration # 97\nCurrent pose score: 10.456\nLowest pose score: 8.219\nIteration # 98\nCurrent pose score: 10.456\nLowest pose score: 8.219\nIteration # 99\nCurrent pose score: 10.080\nLowest pose score: 8.219\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1805544349 seed_offset=0 real_seed=1805544349\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1805544349 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.89626 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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.342013 seconds to load from binary\n[NbConvertApp] Converting notebook 04.01-Basic-Folding-Algorithm.ipynb to python\n[NbConvertApp] Writing 8759 bytes to 04.01-Basic-Folding-Algorithm.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "04.02-Low-Res-Scoring-and-Fragments": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 04.02-Low-Res-Scoring-and-Fragments.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 04.02-Low-Res-Scoring-and-Fragments.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1902401096 seed_offset=0 real_seed=-1902401096\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1902401096 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=542861187 seed_offset=0 real_seed=542861187\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=542861187 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.6026 seconds.\ncore.import_pose.import_pose: File 'inputs/6Q21_A.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.306043 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 0.027143 seconds.\nbasic.io.database: Database file opened: scoriPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\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\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\nng/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 inputs/3mer.frags\n00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 [NbConvertApp] Converting notebook 04.02-Low-Res-Scoring-and-Fragments.ipynb to python\n[NbConvertApp] Writing 11025 bytes to 04.02-Low-Res-Scoring-and-Fragments.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "05.00-Structure-Refinement": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 05.00-Structure-Refinement.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 05.00-Structure-Refinement.py\n[NbConvertApp] Converting notebook 05.00-Structure-Refinement.ipynb to python\n[NbConvertApp] Writing 2958 bytes to 05.00-Structure-Refinement.py\n", "state": "passed"}, "05.01-High-Res-Movers": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 05.01-High-Res-Movers.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 05.01-High-Res-Movers.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1664059858 seed_offset=0 real_seed=1664059858\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1664059858 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1772760947 seed_offset=0 real_seed=1772760947\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1772760947 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.28242 seconds.\ncore.import_pose.import_pose: File 'inputs/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: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: current variant for 134 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 134 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: current variant for 235 CYS\ncore.conformation.Conformation: current variant for 308 CYS\ncore.conformation.Conformation: current variant for 235 CYD\ncore.conformation.Conformation: current variant for 308 CYD\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: current variant for 359 CYS\ncore.conformation.Conformation: current variant for 415 CYS\ncore.conformation.Conformation: current variant for 359 CYD\ncore.conformation.Conformation: current variant for 415 CYD\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: current variant for 457 CYS\ncore.conformation.Conformation: current variant for 522 CYS\ncore.conformation.Conformation: current variant for 457 CYD\ncore.conformation.Conformation: current variant for 522 CYD\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: current variant for 568 CYS\ncore.conformation.Conformation: current variant for 628 CYS\ncore.conformation.Conformation: current variant for 568 CYD\ncore.conformation.Conformation: current variant for 628 CYD\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: current variant for 669 CYS\ncore.conformation.Conformation: current variant for 742 CYS\ncore.conformation.Conformation: current variant for 669 CYD\ncore.conformation.Conformation: current variant for 742 CYD\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.conformation.Conformation: current variant for 793 CYS\ncore.conformation.Conformation: current variant for 849 CYS\ncore.conformation.Conformation: current variant for 793 CYD\ncore.conformation.Conformation: current variant for 849 CYD\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packaPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<class 'pyrosetta.rosetta.protocols.simple_moves.SmallMover'>\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\n3\n0.2727272727272727\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: RepeatMover, Mover type: RepeatMover, Mover current tag: NoTag\nMover being repeated: TrialMover, nmoves: 3\n\nges/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.263756 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\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.TrialMover: Acceptance rate: 0.272727\n[NbConvertApp] Converting notebook 05.01-High-Res-Movers.ipynb to python\n[NbConvertApp] Writing 18044 bytes to 05.01-High-Res-Movers.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "05.02-Refinement-Protocol": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 05.02-Refinement-Protocol.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 05.02-Refinement-Protocol.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=359533926 seed_offset=0 real_seed=359533926\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=359533926 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1142941335 seed_offset=0 real_seed=1142941335\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1142941335 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 1.82359 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.import_pose.import_pose: File 'inputs/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: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: current variant for 134 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 134 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: current variant for 235 CYS\ncore.conformation.Conformation: current variant for 308 CYS\ncore.conformation.Conformation: current variant for 235 CYD\ncore.conformation.Conformation: current variant for 308 CYD\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: current variant for 359 CYS\ncore.conformation.Conformation: current variant for 415 CYS\ncore.conformation.Conformation: current variant for 359 CYD\ncore.conformation.Conformation: current variant for 415 CYD\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: current variant for 457 CYS\ncore.conformation.Conformation: current variant for 522 CYS\ncore.conformation.Conformation: current variant for 457 CYD\ncore.conformation.Conformation: current variant for 522 CYD\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: current variant for 568 CYS\ncore.conformation.Conformation: current variant for 628 CYS\ncore.conformation.Conformation: current variant for 568 CYD\ncore.conformation.Conformation: current variant for 628 CYD\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: current variant for 669 CYS\ncore.conformation.Conformation: current variant for 742 CYS\ncore.conformation.Conformation: current variant for 669 CYD\ncore.conformation.Conformation: current variant for 742 CYD\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.conformation.Conformation: current variant for 793 CYS\ncore.conformation.Conformation: current variant for 849 CYS\ncore.conformation.Conformation: current variant for 793 CYD\ncore.conformation.Conformation: current variant for 849 CYD\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\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: /home/benchmark/workinPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ng_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.332406 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.040\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.051\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.265\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.559\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.581\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\n[NbConvertApp] Converting notebook 05.02-Refinement-Protocol.ipynb to python\n[NbConvertApp] Writing 5272 bytes to 05.02-Refinement-Protocol.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "06.00-Introduction-to-Packing-and-Design": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.00-Introduction-to-Packing-and-Design.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.00-Introduction-to-Packing-and-Design.py\n[NbConvertApp] Converting notebook 06.00-Introduction-to-Packing-and-Design.ipynb to python\n[NbConvertApp] Writing 3085 bytes to 06.00-Introduction-to-Packing-and-Design.py\n", "state": "passed"}, "06.01-Side-Chain-Conformations-and-Dunbrack-Energies": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.01-Side-Chain-Conformations-and-Dunbrack-Energies.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1467977689 seed_offset=0 real_seed=-1467977689\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1467977689 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1807749333 seed_offset=0 real_seed=-1807749333\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1807749333 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.79013 seconds.\ncore.import_pose.import_pose: File 'inputs/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: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 134 194\ncore.conformation.Conformation: current variant for 134 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 134 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 235 308\ncore.conformation.Conformation: current variant for 235 CYS\ncore.conformation.Conformation: current variant for 308 CYS\ncore.conformation.Conformation: current variant for 235 CYD\ncore.conformation.Conformation: current variant for 308 CYD\ncore.conformation.Conformation: Found disulfide between residues 359 415\ncore.conformation.Conformation: current variant for 359 CYS\ncore.conformation.Conformation: current variant for 415 CYS\ncore.conformation.Conformation: current variant for 359 CYD\ncore.conformation.Conformation: current variant for 415 CYD\ncore.conformation.Conformation: Found disulfide between residues 457 522\ncore.conformation.Conformation: current variant for 457 CYS\ncore.conformation.Conformation: current variant for 522 CYS\ncore.conformation.Conformation: current variant for 457 CYD\ncore.conformation.Conformation: current variant for 522 CYD\ncore.conformation.Conformation: Found disulfide between residues 568 628\ncore.conformation.Conformation: current variant for 568 CYS\ncore.conformation.Conformation: current variant for 628 CYS\ncore.conformation.Conformation: current variant for 568 CYD\ncore.conformation.Conformation: current variant for 628 CYD\ncore.conformation.Conformation: Found disulfide between residues 669 742\ncore.conformation.Conformation: current variant for 669 CYS\ncore.conformation.Conformation: current variant for 742 CYS\ncore.conformation.Conformation: current variant for 669 CYD\ncore.conformation.Conformation: current variant for 742 CYD\ncore.conformation.Conformation: Found disulfide between residues 793 849\ncore.conformation.Conformation: current variant for 793 CYS\ncore.conformation.Conformation: current variant for 849 CYS\ncore.conformation.Conformation: current variant for 793 CYD\ncore.conformation.Conformation: current variant for 849 CYD\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-paPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nLYS\nPhi: -122.41752\nPsi: 153.08267\n\nChi 1: 68.12458\nChi 2: -169.18576\nChi 3: -175.37028\nChi 4: -169.58806\n( fa_atr; -8.83354) ( fa_rep; 2.78019) ( fa_sol; 5.92847) ( fa_intra_atr; -1.68168) ( fa_intra_rep; 2.47533) ( fa_intra_sol; 1.20218) ( fa_intra_atr_xover4; -0.52776) ( fa_intra_rep_xover4; 0.191981) ( fa_intra_sol_xover4; 0.292855) ( fa_intra_atr_nonprotein; 0) ( fa_intra_rep_nonprotein; 0) ( fa_intra_sol_nonprotein; 0) ( fa_intra_RNA_base_phos_atr; 0) ( fa_intra_RNA_base_phos_rep; 0) ( fa_intra_RNA_base_phos_sol; 0) ( fa_atr_dummy; 0) ( fa_rep_dummy; 0) ( fa_sol_dummy; 0) ( fa_vdw_tinker; 0) ( lk_hack; 0) ( lk_ball; 0) ( lk_ball_wtd; 0.321463) ( lk_ball_iso; 0) ( lk_ball_bridge; 0) ( lk_ball_bridge_uncpl; 0) ( lk_dome; 0) ( lk_dome_iso; 0) ( lk_dome_bridge; 0) ( lk_dome_bridge_uncpl; 0) ( lk_ball_bridge2; 0) ( lk_ball_bridge_uncpl2; 0) ( lk_dome_pack; 0) ( coarse_fa_atr; 0) ( coarse_fa_rep; 0) ( coarse_fa_sol; 0) ( coarse_beadlj; 0) ( mm_lj_intra_rep; 0) ( mm_lj_intra_atr; 0) ( mm_lj_inter_rep; 0) ( mm_lj_inter_atr; 0) ( mm_twist; 0) ( mm_bend; 0) ( mm_stretch; 0) ( lk_costheta; 0) ( lk_polar; 0) ( lk_nonpolar; 0) ( lk_polar_intra_RNA; 0) ( lk_nonpolar_intra_RNA; 0) ( fa_elec; -2.75782) ( fa_elec_bb_bb; 0) ( fa_elec_bb_sc; 0) ( fa_elec_sc_sc; 0) ( fa_intra_elec; 0) ( h2o_hbond; 0) ( dna_dr; 0) ( dna_bp; 0) ( dna_bs; 0) ( dna_ref; 0) ( peptide_bond; 0) ( pcs; 0) ( pcsTs1; 0) ( pcsTs2; 0) ( pcsTs3; 0) ( pcsTs4; 0) ( pcs2; 0) ( fastsaxs; 0) ( saxs_score; 0) ( saxs_cen_score; 0) ( saxs_fa_score; 0) ( pddf_score; 0) ( fiberdiffraction; 0) ( fiberdiffractiondens; 0) ( epr_deer_score; 0) ( fa_mbenv; 0) ( fa_mbsolv; 0) ( fa_elec_rna_phos_phos; 0) ( fa_elec_rna_phos_sugr; 0) ( fa_elec_rna_phos_base; 0) ( fa_elec_rna_sugr_sugr; 0) ( fa_elec_rna_sugr_base; 0) ( fa_elec_rna_base_base; 0) ( fa_elec_rna_phos_phos_fast; 0) ( fa_elec_rna_phos_sugr_fast; 0) ( fa_elec_rna_phos_base_fast; 0) ( fa_elec_rna_sugr_sugr_fast; 0) ( fa_elec_rna_sugr_base_fast; 0) ( fa_elec_rna_base_base_fast; 0) ( fa_elec_aro_aro; 0) ( fa_elec_aro_all; 0) ( hack_aro; 0) ( rna_fa_atr_base; 0) ( rna_fa_rep_base; 0) ( rna_data_backbone; 0) ( ch_bond; 0) ( ch_bond_bb_bb; 0) ( ch_bond_sc_sc; 0) ( ch_bond_bb_sc; 0) ( pro_close; 0) ( rama2b; 0) ( vdw; 0) ( cenpack; 0) ( cenpack_smooth; 0) ( cen_hb; 0) ( hybrid_vdw; 0) ( gauss; 0) ( rna_vdw; 0) ( rnp_vdw; 0) ( rna_base_backbone; 0) ( rna_backbone_backbone; 0) ( rna_repulsive; 0) ( rna_base_pair_pairwise; 0) ( rna_base_axis_pairwise; 0) ( rna_base_stagger_pairwise; 0) ( rna_base_stack_pairwise; 0) ( rna_base_stack_axis_pairwise; 0) ( rna_data_base; 0) ( rna_base_pair; 0) ( rna_base_axis; 0) ( rna_base_stagger; 0) ( rna_base_stack; 0) ( rna_base_stack_axis; 0) ( rnp_base_pair; 0) ( rnp_stack; 0) ( rnp_stack_xy; 0) ( rnp_pair; 0) ( rnp_pair_dist; 0) ( rnp_aa_to_rna_backbone; 0) ( rna_mg_point; 0) ( rna_mg_point_indirect; 0) ( mg; 0) ( mg_lig; 0) ( mg_sol; 0) ( mg_ref; 0) ( hoh_ref; 0) ( rna_torsion; 0) ( rna_torsion_sc; 0) ( rna_suite; 0) ( rna_jr_suite; 0) ( suiteness_bonus; 0) ( tna_suite; 0) ( rna_sugar_close; 0) ( fa_stack; 0) ( fa_stack_lower; 0) ( fa_stack_upper; 0) ( fa_stack_aro; 0) ( fa_stack_ext; 0) ( fa_stack_sol; 0) ( fa_stack_lr; 0) ( fa_stack_rna_protein; 0) ( fa_stack_rna_protein_aro; 0) ( ss_contact_worst; 0) ( stack_elec; 0) ( stack_elec_base_base; 0) ( stack_elec_base_bb; 0) ( alignment; 0) ( dna_bb_torsion; 0) ( dna_sugar_close; 0) ( dna_base_distance; 0) ( geom_sol_fast; 0) ( geom_sol_fast_intra_RNA; 0) ( fa_cust_pair_dist; 0) ( custom_atom_pair; 0) ( orbitals_hpol_bb; 0) ( pci_cation_pi; 0) ( pci_pi_pi; 0) ( pci_salt_bridge; 0) ( pci_hbond; 0) ( arg_cation_pi; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_first; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_170; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_171; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_172; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_173; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_174; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_175; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_176; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_177; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_178; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_last; 0) ( python; 0) ( fa_pair; 0) ( fa_pair_aro_aro; 0) ( fa_pair_aro_pol; 0) ( fa_pair_pol_pol; 0) ( hbond_sr_bb; 0) ( hbond_lr_bb; 0) ( hbond_bb_sc; 0) ( hbond_sr_bb_sc; 0) ( hbond_lr_bb_sc; 0) ( hbond_sc; 0) ( hbond_intra; 0) ( hbond_wat; 0) ( wat_entropy; 0) ( hbond; 0) ( npd_hbond_sr_bb; 0) ( npd_hbond_lr_bb; 0) ( npd_hbond_bb_sc; 0) ( npd_hbond_sr_bb_sc; 0) ( npd_hbond_lr_bb_sc; 0) ( npd_hbond_sc; 0) ( npd_hbond_intra; 0) ( npd_hbond; 0) ( fa_grpelec; 0) ( PyRosettaTwoBodyContextDependentEnergy_first; 0) ( PyRosettaTwoBodyContextDependentEnergy_205; 0) ( PyRosettaTwoBodyContextDependentEnergy_206; 0) ( PyRosettaTwoBodyContextDependentEnergy_207; 0) ( PyRosettaTwoBodyContextDependentEnergy_208; 0) ( PyRosettaTwoBodyContextDependentEnergy_209; 0) ( PyRosettaTwoBodyContextDependentEnergy_210; 0) ( PyRosettaTwoBodyContextDependentEnergy_211; 0) ( PyRosettaTwoBodyContextDependentEnergy_212; 0) ( PyRosettaTwoBodyContextDependentEnergy_213; 0) ( PyRosettaTwoBodyContextDependentEnergy_last; 0) ( interface_dd_pair; 0) ( geom_sol; 0) ( geom_sol_intra_RNA; 0) ( occ_sol_fitted; 0) ( occ_sol_fitted_onebody; 0) ( occ_sol_exact; 0) ( cen_rot_pair; 0) ( cen_rot_pair_ang; 0) ( cen_rot_pair_dih; 0) ( pair; 0) ( cen_pair_smooth; 0) ( Mpair; 0) ( mp_pair; 0) ( fa_mpsolv; 0) ( suck; 0) ( rna_rg; 0) ( rna_motif; 0) ( facts_elec; 0) ( facts_solv; 0) ( facts_sasa; 0) ( motif_dock; 0) ( pointwater; 0) ( goap; 0) ( goap_dist; 0) ( goap_angle; 0) ( approximate_buried_unsat_penalty; 0) ( interchain_pair; 0) ( interchain_vdw; 0) ( gb_elec; 0) ( multipole_elec; 0) ( fa_sasa; 0) ( dslf_ss_dst; 0) ( dslf_cs_ang; 0) ( dslf_ss_dih; 0) ( dslf_ca_dih; 0) ( dslf_cbs_ds; 0) ( dslf_fa13; 0) ( dslfc_cen_dst; 0) ( dslfc_cb_dst; 0) ( dslfc_ang; 0) ( dslfc_cb_dih; 0) ( dslfc_bb_dih; 0) ( dslfc_rot; 0) ( dslfc_trans; 0) ( dslfc_RT; 0) ( atom_pair_constraint; 0) ( base_pair_constraint; 0) ( coarse_chainbreak_constraint; 0) ( constant_constraint; 0) ( coordinate_constraint; 0) ( angle_constraint; 0) ( dihedral_constraint; 0) ( big_bin_constraint; 0) ( dunbrack_constraint; 0) ( site_constraint; 0) ( metalhash_constraint; 0) ( metalbinding_constraint; 0) ( rna_stub_coord_hack; 0) ( bond_geometry; 0) ( rna_bond_geometry; 0) ( Hpol_bond_geometry; 0) ( rama; 0) ( omega; 0.0116849) ( fa_dun; 3.97212) ( fa_dun_dev; 1.07017) ( fa_dun_rot; 2.90195) ( fa_dun_semi; 0) ( cen_rot_dun; 0) ( dna_chi; 0) ( p_aa_pp; 0.0112208) ( p_aa_ss; 0) ( yhh_planarity; 0) ( hxl_tors; 0) ( h2o_intra; 0) ( ref; -0.71458) ( ref_nc; 0) ( seqdep_ref; 0) ( nmer_ref; 0) ( nmer_pssm; 0) ( nmer_svm; 0) ( envsmooth; 0) ( e_pH; 0) ( rna_bulge; 0) ( dna_dihedral_bb; 0) ( dna_dihedral_chi; 0) ( dna_dihedral_sugar; 0) ( sugar_bb; 0) ( free_suite; 0) ( free_2HOprime; 0) ( free_side_chain; 0) ( free_base; 0) ( free_res; 0) ( free_dof; 0) ( intermol; 0) ( other_pose; 0) ( special_rot; 0) ( PB_elec; 0) ( cen_env_smooth; 0) ( cbeta_smooth; 0) ( cen_rot_env; 0) ( cen_rot_cbeta; 0) ( env; 0) ( cbeta; 0) ( DFIRE; 0) ( Menv; 0) ( Mcbeta; 0) ( Menv_non_helix; 0) ( Menv_termini; 0) ( Menv_tm_proj; 0) ( Mlipo; 0) ( rg; 0) ( rg_local; 0) ( co; 0) ( hs_pair; 0) ( ss_pair; 0) ( rsigma; 0) ( sheet; 0) ( burial_v2; 0) ( burial; 0) ( abego; 0) ( covalent_labeling; 0) ( covalent_labeling_fa; 0) ( hrf_ms_labeling; 0) ( hrf_dynamics; 0) ( ccs_imms; 0) ( depc_ms; 0) ( rnp_env; 0) ( loop_close; 0) ( missing_res; 0) ( mp_env; 0) ( mp_cbeta; 0) ( mp_lipo; 0) ( mp_termini; 0) ( mp_nonhelix; 0) ( mp_tmproj; 0) ( fa_mpenv; 0) ( fa_mpenv_smooth; 0) ( fa_water_to_bilayer; 0) ( fa_mpasymEzCB; 0) ( fa_mpasymEzCG; 0) ( mp_res_lipo; 0) ( span_ins; 0) ( mp_span_ang; 0) ( mp_helicality; 0) ( natbias_ss; 0) ( natbias_hs; 0) ( natbias_hh; 0) ( natbias_stwist; 0) ( aa_cmp; 0) ( dock_ens_conf; 0) ( csa; 0) ( dc; 0) ( rdc; 0) ( rdc_segments; 0) ( rdc_rohl; 0) ( nmr_pcs; 0) ( nmr_rdc; 0) ( nmr_pre; 0) ( cen_pair_motifs; 0) ( cen_pair_motif_degree; 0) ( holes; 0) ( holes_decoy; 0) ( holes_resl; 0) ( holes_min; 0) ( holes_min_mean; 0) ( rna_chem_shift; 0) ( rna_chem_map; 0) ( rna_chem_map_lores; 0) ( rna_partition; 0) ( dab_sasa; 0) ( dab_sev; 0) ( sa; 0) ( d2h_sa; 0) ( ProQM; 0) ( ProQ; 0) ( interchain_env; 0) ( interchain_contact; 0) ( chainbreak; 0) ( linear_chainbreak; 0) ( overlap_chainbreak; 0) ( distance_chainbreak; 0) ( dof_constraint; 0) ( branch_conn; 0) ( linear_branch_conn; 0) ( rama_prepro; -0.0498918) ( paa_abego3; 0) ( cart_bonded; 0) ( cart_bonded_angle; 0) ( cart_bonded_length; 0) ( cart_bonded_ring; 0) ( cart_bonded_torsion; 0) ( cart_bonded_proper; 0) ( cart_bonded_improper; 0) ( gen_bonded; 0) ( gen_bonded_bond; 0) ( gen_bonded_angle; 0) ( gen_bonded_torsion; 0) ( gen_bonded_improper; 0) ( neigh_vect; 0) ( neigh_count; 0) ( neigh_vect_raw; 0) ( symE_bonus; 0) ( sym_lig; 0) ( mhc_epitope; 0) ( pack_stat; 0) ( rms_energy; 0) ( res_type_constraint; 0) ( res_type_linking_constraint; 0) ( pocket_constraint; 0) ( backbone_stub_constraint; 0) ( backbone_stub_linear_constraint; 0) ( surface; 0) ( p_aa; 0) ( unfolded; 0) ( split_unfolded_two_body; 0) ( fa_atr_ref; 0) ( fa_rep_ref; 0) ( fa_sol_ref; 0) ( fa_elec_ref; 0) ( hbond_ref; 0) ( dslf_fa13_ref; 0) ( fa_intra_atr_ref; 0) ( fa_intra_rep_ref; 0) ( fa_intra_sol_ref; 0) ( pro_close_ref; 0) ( fa_dun_ref; 0) ( fa_dun_dev_ref; 0) ( fa_dun_rot_ref; 0) ( fa_dun_semi_ref; 0) ( rama_ref; 0) ( p_aa_pp_ref; 0) ( omega_ref; 0) ( mm_lj_intra_rep_ref; 0) ( mm_lj_intra_atr_ref; 0) ( mm_twist_ref; 0) ( elec_dens_fast; 0) ( elec_dens_window; 0) ( elec_dens_whole_structure_ca; 0) ( elec_dens_whole_structure_allatom; 0) ( elec_dens_atomwise; 0) ( grid_vdw; 0) ( xtal_ml; 0) ( xtal_rwork; 0) ( xtal_rfree; 0) ( hpatch; 0) ( Menv_smooth; 0) ( wat_desolv; 0) ( ring_close; 0) ( aa_repeat; 0) ( aa_composition; 0) ( aspartimide_penalty; 0) ( hbnet; 0) ( buried_unsatisfied_penalty; 0) ( netcharge; 0) ( voids_penalty; 0) ( sap_constraint; 0) ( dna_env; 0) ( dna_pair; 0) ( dump_trajectory; 0) ( PyRosettaEnergy_first; 0) ( PyRosettaEnergy_475; 0) ( PyRosettaEnergy_476; 0) ( PyRosettaEnergy_477; 0) ( PyRosettaEnergy_478; 0) ( PyRosettaEnergy_479; 0) ( PyRosettaEnergy_480; 0) ( PyRosettaEnergy_481; 0) ( PyRosettaEnergy_482; 0) ( PyRosettaEnergy_483; 0) ( PyRosettaEnergy_last; 0) ( sidechain_neighbors; 0) ( target_clash; 0) ( membrane_span_constraint; 0) ( membrane_span_term_z_constraint; 0) ( aromatic_restraint; 0) ( rna_coarse_dist; 0) ( total_score; -1.45222) ( dummy_score_type; 0) \n3.9721243480599373\n( fa_atr; -11.6375) ( fa_rep; 789.493) ( fa_sol; 11.6773) ( fa_intra_atr; -1.44441) ( fa_intra_rep; 1.80557) ( fa_intra_sol; 0.785201) ( fa_intra_atr_xover4; -0.343391) ( fa_intra_rep_xover4; 0.112709) ( fa_intra_sol_xover4; 0.105435) ( fa_intra_atr_nonprotein; 0) ( fa_intra_rep_nonprotein; 0) ( fa_intra_sol_nonprotein; 0) ( fa_intra_RNA_base_phos_atr; 0) ( fa_intra_RNA_base_phos_rep; 0) ( fa_intra_RNA_base_phos_sol; 0) ( fa_atr_dummy; 0) ( fa_rep_dummy; 0) ( fa_sol_dummy; 0) ( fa_vdw_tinker; 0) ( lk_hack; 0) ( lk_ball; 0) ( lk_ball_wtd; 0.302965) ( lk_ball_iso; 0) ( lk_ball_bridge; 0) ( lk_ball_bridge_uncpl; 0) ( lk_dome; 0) ( lk_dome_iso; 0) ( lk_dome_bridge; 0) ( lk_dome_bridge_uncpl; 0) ( lk_ball_bridge2; 0) ( lk_ball_bridge_uncpl2; 0) ( lk_dome_pack; 0) ( coarse_fa_atr; 0) ( coarse_fa_rep; 0) ( coarse_fa_sol; 0) ( coarse_beadlj; 0) ( mm_lj_intra_rep; 0) ( mm_lj_intra_atr; 0) ( mm_lj_inter_rep; 0) ( mm_lj_inter_atr; 0) ( mm_twist; 0) ( mm_bend; 0) ( mm_stretch; 0) ( lk_costheta; 0) ( lk_polar; 0) ( lk_nonpolar; 0) ( lk_polar_intra_RNA; 0) ( lk_nonpolar_intra_RNA; 0) ( fa_elec; -9.02391) ( fa_elec_bb_bb; 0) ( fa_elec_bb_sc; 0) ( fa_elec_sc_sc; 0) ( fa_intra_elec; 0) ( h2o_hbond; 0) ( dna_dr; 0) ( dna_bp; 0) ( dna_bs; 0) ( dna_ref; 0) ( peptide_bond; 0) ( pcs; 0) ( pcsTs1; 0) ( pcsTs2; 0) ( pcsTs3; 0) ( pcsTs4; 0) ( pcs2; 0) ( fastsaxs; 0) ( saxs_score; 0) ( saxs_cen_score; 0) ( saxs_fa_score; 0) ( pddf_score; 0) ( fiberdiffraction; 0) ( fiberdiffractiondens; 0) ( epr_deer_score; 0) ( fa_mbenv; 0) ( fa_mbsolv; 0) ( fa_elec_rna_phos_phos; 0) ( fa_elec_rna_phos_sugr; 0) ( fa_elec_rna_phos_base; 0) ( fa_elec_rna_sugr_sugr; 0) ( fa_elec_rna_sugr_base; 0) ( fa_elec_rna_base_base; 0) ( fa_elec_rna_phos_phos_fast; 0) ( fa_elec_rna_phos_sugr_fast; 0) ( fa_elec_rna_phos_base_fast; 0) ( fa_elec_rna_sugr_sugr_fast; 0) ( fa_elec_rna_sugr_base_fast; 0) ( fa_elec_rna_base_base_fast; 0) ( fa_elec_aro_aro; 0) ( fa_elec_aro_all; 0) ( hack_aro; 0) ( rna_fa_atr_base; 0) ( rna_fa_rep_base; 0) ( rna_data_backbone; 0) ( ch_bond; 0) ( ch_bond_bb_bb; 0) ( ch_bond_sc_sc; 0) ( ch_bond_bb_sc; 0) ( pro_close; 0) ( rama2b; 0) ( vdw; 0) ( cenpack; 0) ( cenpack_smooth; 0) ( cen_hb; 0) ( hybrid_vdw; 0) ( gauss; 0) ( rna_vdw; 0) ( rnp_vdw; 0) ( rna_base_backbone; 0) ( rna_backbone_backbone; 0) ( rna_repulsive; 0) ( rna_base_pair_pairwise; 0) ( rna_base_axis_pairwise; 0) ( rna_base_stagger_pairwise; 0) ( rna_base_stack_pairwise; 0) ( rna_base_stack_axis_pairwise; 0) ( rna_data_base; 0) ( rna_base_pair; 0) ( rna_base_axis; 0) ( rna_base_stagger; 0) ( rna_base_stack; 0) ( rna_base_stack_axis; 0) ( rnp_base_pair; 0) ( rnp_stack; 0) ( rnp_stack_xy; 0) ( rnp_pair; 0) ( rnp_pair_dist; 0) ( rnp_aa_to_rna_backbone; 0) ( rna_mg_point; 0) ( rna_mg_point_indirect; 0) ( mg; 0) ( mg_lig; 0) ( mg_sol; 0) ( mg_ref; 0) ( hoh_ref; 0) ( rna_torsion; 0) ( rna_torsion_sc; 0) ( rna_suite; 0) ( rna_jr_suite; 0) ( suiteness_bonus; 0) ( tna_suite; 0) ( rna_sugar_close; 0) ( fa_stack; 0) ( fa_stack_lower; 0) ( fa_stack_upper; 0) ( fa_stack_aro; 0) ( fa_stack_ext; 0) ( fa_stack_sol; 0) ( fa_stack_lr; 0) ( fa_stack_rna_protein; 0) ( fa_stack_rna_protein_aro; 0) ( ss_contact_worst; 0) ( stack_elec; 0) ( stack_elec_base_base; 0) ( stack_elec_base_bb; 0) ( alignment; 0) ( dna_bb_torsion; 0) ( dna_sugar_close; 0) ( dna_base_distance; 0) ( geom_sol_fast; 0) ( geom_sol_fast_intra_RNA; 0) ( fa_cust_pair_dist; 0) ( custom_atom_pair; 0) ( orbitals_hpol_bb; 0) ( pci_cation_pi; 0) ( pci_pi_pi; 0) ( pci_salt_bridge; 0) ( pci_hbond; 0) ( arg_cation_pi; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_first; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_170; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_171; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_172; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_173; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_174; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_175; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_176; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_177; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_178; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_last; 0) ( python; 0) ( fa_pair; 0) ( fa_pair_aro_aro; 0) ( fa_pair_aro_pol; 0) ( fa_pair_pol_pol; 0) ( hbond_sr_bb; 0) ( hbond_lr_bb; 0) ( hbond_bb_sc; 0) ( hbond_sr_bb_sc; 0) ( hbond_lr_bb_sc; 0) ( hbond_sc; -0.274355) ( hbond_intra; 0) ( hbond_wat; 0) ( wat_entropy; 0) ( hbond; 0) ( npd_hbond_sr_bb; 0) ( npd_hbond_lr_bb; 0) ( npd_hbond_bb_sc; 0) ( npd_hbond_sr_bb_sc; 0) ( npd_hbond_lr_bb_sc; 0) ( npd_hbond_sc; 0) ( npd_hbond_intra; 0) ( npd_hbond; 0) ( fa_grpelec; 0) ( PyRosettaTwoBodyContextDependentEnergy_first; 0) ( PyRosettaTwoBodyContextDependentEnergy_205; 0) ( PyRosettaTwoBodyContextDependentEnergy_206; 0) ( PyRosettaTwoBodyContextDependentEnergy_207; 0) ( PyRosettaTwoBodyContextDependentEnergy_208; 0) ( PyRosettaTwoBodyContextDependentEnergy_209; 0) ( PyRosettaTwoBodyContextDependentEnergy_210; 0) ( PyRosettaTwoBodyContextDependentEnergy_211; 0) ( PyRosettaTwoBodyContextDependentEnergy_212; 0) ( PyRosettaTwoBodyContextDependentEnergy_213; 0) ( PyRosettaTwoBodyContextDependentEnergy_last; 0) ( interface_dd_pair; 0) ( geom_sol; 0) ( geom_sol_intra_RNA; 0) ( occ_sol_fitted; 0) ( occ_sol_fitted_onebody; 0) ( occ_sol_exact; 0) ( cen_rot_pair; 0) ( cen_rot_pair_ang; 0) ( cen_rot_pair_dih; 0) ( pair; 0) ( cen_pair_smooth; 0) ( Mpair; 0) ( mp_pair; 0) ( fa_mpsolv; 0) ( suck; 0) ( rna_rg; 0) ( rna_motif; 0) ( facts_elec; 0) ( facts_solv; 0) ( facts_sasa; 0) ( motif_dock; 0) ( pointwater; 0) ( goap; 0) ( goap_dist; 0) ( goap_angle; 0) ( approximate_buried_unsat_penalty; 0) ( interchain_pair; 0) ( interchain_vdw; 0) ( gb_elec; 0) ( multipole_elec; 0) ( fa_sasa; 0) ( dslf_ss_dst; 0) ( dslf_cs_ang; 0) ( dslf_ss_dih; 0) ( dslf_ca_dih; 0) ( dslf_cbs_ds; 0) ( dslf_fa13; 0) ( dslfc_cen_dst; 0) ( dslfc_cb_dst; 0) ( dslfc_ang; 0) ( dslfc_cb_dih; 0) ( dslfc_bb_dih; 0) ( dslfc_rot; 0) ( dslfc_trans; 0) ( dslfc_RT; 0) ( atom_pair_constraint; 0) ( base_pair_constraint; 0) ( coarse_chainbreak_constraint; 0) ( constant_constraint; 0) ( coordinate_constraint; 0) ( angle_constraint; 0) ( dihedral_constraint; 0) ( big_bin_constraint; 0) ( dunbrack_constraint; 0) ( site_constraint; 0) ( metalhash_constraint; 0) ( metalbinding_constraint; 0) ( rna_stub_coord_hack; 0) ( bond_geometry; 0) ( rna_bond_geometry; 0) ( Hpol_bond_geometry; 0) ( rama; 0) ( omega; 0.0116849) ( fa_dun; 3.79108) ( fa_dun_dev; 0.030004) ( fa_dun_rot; 3.76108) ( fa_dun_semi; 0) ( cen_rot_dun; 0) ( dna_chi; 0) ( p_aa_pp; 0.0112208) ( p_aa_ss; 0) ( yhh_planarity; 0) ( hxl_tors; 0) ( h2o_intra; 0) ( ref; -0.71458) ( ref_nc; 0) ( seqdep_ref; 0) ( nmer_ref; 0) ( nmer_pssm; 0) ( nmer_svm; 0) ( envsmooth; 0) ( e_pH; 0) ( rna_bulge; 0) ( dna_dihedral_bb; 0) ( dna_dihedral_chi; 0) ( dna_dihedral_sugar; 0) ( sugar_bb; 0) ( free_suite; 0) ( free_2HOprime; 0) ( free_side_chain; 0) ( free_base; 0) ( free_res; 0) ( free_dof; 0) ( intermol; 0) ( other_pose; 0) ( special_rot; 0) ( PB_elec; 0) ( cen_env_smooth; 0) ( cbeta_smooth; 0) ( cen_rot_env; 0) ( cen_rot_cbeta; 0) ( env; 0) ( cbeta; 0) ( DFIRE; 0) ( Menv; 0) ( Mcbeta; 0) ( Menv_non_helix; 0) ( Menv_termini; 0) ( Menv_tm_proj; 0) ( Mlipo; 0) ( rg; 0) ( rg_local; 0) ( co; 0) ( hs_pair; 0) ( ss_pair; 0) ( rsigma; 0) ( sheet; 0) ( burial_v2; 0) ( burial; 0) ( abego; 0) ( covalent_labeling; 0) ( covalent_labeling_fa; 0) ( hrf_ms_labeling; 0) ( hrf_dynamics; 0) ( ccs_imms; 0) ( depc_ms; 0) ( rnp_env; 0) ( loop_close; 0) ( missing_res; 0) ( mp_env; 0) ( mp_cbeta; 0) ( mp_lipo; 0) ( mp_termini; 0) ( mp_nonhelix; 0) ( mp_tmproj; 0) ( fa_mpenv; 0) ( fa_mpenv_smooth; 0) ( fa_water_to_bilayer; 0) ( fa_mpasymEzCB; 0) ( fa_mpasymEzCG; 0) ( mp_res_lipo; 0) ( span_ins; 0) ( mp_span_ang; 0) ( mp_helicality; 0) ( natbias_ss; 0) ( natbias_hs; 0) ( natbias_hh; 0) ( natbias_stwist; 0) ( aa_cmp; 0) ( dock_ens_conf; 0) ( csa; 0) ( dc; 0) ( rdc; 0) ( rdc_segments; 0) ( rdc_rohl; 0) ( nmr_pcs; 0) ( nmr_rdc; 0) ( nmr_pre; 0) ( cen_pair_motifs; 0) ( cen_pair_motif_degree; 0) ( holes; 0) ( holes_decoy; 0) ( holes_resl; 0) ( holes_min; 0) ( holes_min_mean; 0) ( rna_chem_shift; 0) ( rna_chem_map; 0) ( rna_chem_map_lores; 0) ( rna_partition; 0) ( dab_sasa; 0) ( dab_sev; 0) ( sa; 0) ( d2h_sa; 0) ( ProQM; 0) ( ProQ; 0) ( interchain_env; 0) ( interchain_contact; 0) ( chainbreak; 0) ( linear_chainbreak; 0) ( overlap_chainbreak; 0) ( distance_chainbreak; 0) ( dof_constraint; 0) ( branch_conn; 0) ( linear_branch_conn; 0) ( rama_prepro; -0.0498918) ( paa_abego3; 0) ( cart_bonded; 0) ( cart_bonded_angle; 0) ( cart_bonded_length; 0) ( cart_bonded_ring; 0) ( cart_bonded_torsion; 0) ( cart_bonded_proper; 0) ( cart_bonded_improper; 0) ( gen_bonded; 0) ( gen_bonded_bond; 0) ( gen_bonded_angle; 0) ( gen_bonded_torsion; 0) ( gen_bonded_improper; 0) ( neigh_vect; 0) ( neigh_count; 0) ( neigh_vect_raw; 0) ( symE_bonus; 0) ( sym_lig; 0) ( mhc_epitope; 0) ( pack_stat; 0) ( rms_energy; 0) ( res_type_constraint; 0) ( res_type_linking_constraint; 0) ( pocket_constraint; 0) ( backbone_stub_constraint; 0) ( backbone_stub_linear_constraint; 0) ( surface; 0) ( p_aa; 0) ( unfolded; 0) ( split_unfolded_two_body; 0) ( fa_atr_ref; 0) ( fa_rep_ref; 0) ( fa_sol_ref; 0) ( fa_elec_ref; 0) ( hbond_ref; 0) ( dslf_fa13_ref; 0) ( fa_intra_atr_ref; 0) ( fa_intra_rep_ref; 0) ( fa_intra_sol_ref; 0) ( pro_close_ref; 0) ( fa_dun_ref; 0) ( fa_dun_dev_ref; 0) ( fa_dun_rot_ref; 0) ( fa_dun_semi_ref; 0) ( rama_ref; 0) ( p_aa_pp_ref; 0) ( omega_ref; 0) ( mm_lj_intra_rep_ref; 0) ( mm_lj_intra_atr_ref; 0) ( mm_twist_ref; 0) ( elec_dens_fast; 0) ( elec_dens_window; 0) ( elec_dens_whole_structure_ca; 0) ( elec_dens_whole_structure_allatom; 0) ( elec_dens_atomwise; 0) ( grid_vdw; 0) ( xtal_ml; 0) ( xtal_rwork; 0) ( xtal_rfree; 0) ( hpatch; 0) ( Menv_smooth; 0) ( wat_desolv; 0) ( ring_close; 0) ( aa_repeat; 0) ( aa_composition; 0) ( aspartimide_penalty; 0) ( hbnet; 0) ( buried_unsatisfied_penalty; 0) ( netcharge; 0) ( voids_penalty; 0) ( sap_constraint; 0) ( dna_env; 0) ( dna_pair; 0) ( dump_trajectory; 0) ( PyRosettaEnergy_first; 0) ( PyRosettaEnergy_475; 0) ( PyRosettaEnergy_476; 0) ( PyRosettaEnergy_477; 0) ( PyRosettaEnergy_478; 0) ( PyRosettaEnergy_479; 0) ( PyRosettaEnergy_480; 0) ( PyRosettaEnergy_481; 0) ( PyRosettaEnergy_482; 0) ( PyRosettaEnergy_483; 0) ( PyRosettaEnergy_last; 0) ( sidechain_neighbors; 0) ( target_clash; 0) ( membrane_span_constraint; 0) ( membrane_span_term_z_constraint; 0) ( aromatic_restraint; 0) ( rna_coarse_dist; 0) ( total_score; 427.308) ( dummy_score_type; 0) \n3.7910821714280263\nckages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.357519 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.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n[NbConvertApp] Converting notebook 06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb to python\n[NbConvertApp] Writing 4317 bytes to 06.01-Side-Chain-Conformations-and-Dunbrack-Energies.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "06.02-Packing-design-and-regional-relax": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.02-Packing-design-and-regional-relax.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.02-Packing-design-and-regional-relax.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1167406573 seed_offset=0 real_seed=-1167406573\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1167406573 RG_type=mt19937\ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -use_input_sc -input_ab_scheme AHo_Scheme -ignore_unrecognized_res -ignore_zero_occupancy false -load_PDB_components false -relax:default_repeats 2 -no_fconfig -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-668795310 seed_offset=0 real_seed=-668795310\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-668795310 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.66247 seconds.\ncore.import_pose.import_pose: File 'inputs/2r0l_1_1.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 225\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 464\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 130 204\ncore.conformation.Conformation: current variant for 130 CYS\ncore.conformation.Conformation: current variant for 204 CYS\ncore.conformation.Conformation: current variant for 130 CYD\ncore.conformation.Conformation: current variant for 204 CYD\ncore.conformation.Conformation: Found disulfide between residues 250 266\ncore.conformation.Conformation: current variant for 250 CYS\ncore.conformation.Conformation: current variant for 266 CYS\ncore.conformation.Conformation: current variant for 250 CYD\ncore.conformation.Conformation: current variant for 266 CYD\ncore.conformation.Conformation: Found disulfide between residues 258 328\ncore.conformation.Conformation: current variant for 258 CYS\ncore.conformation.Conformation: current variant for 328 CYS\ncore.conformation.Conformation: current variant for 258 CYD\ncore.conformation.Conformation: current variant for 328 CYD\ncore.conformation.Conformation: Found disulfide between residues 353 422\ncore.conformation.Conformation: current variant for 353 CYS\ncore.conformation.Conformation: current variant for 422 CYS\ncore.conformation.Conformation: current variant for 353 CYD\ncore.conformation.Conformation: current variant for 422 CYD\ncore.conformation.Conformation: Found disulfide between residues 385 401\ncore.conformation.Conformation: current variant for 385 CYS\ncore.conformation.Conformation: current variant for 401 CYS\ncore.conformation.Conformation: current variant for 385 CYD\ncore.conformation.Conformation: current variant for 401 CYD\ncore.conformation.Conformation: Found disulfide between residues 412 440\ncore.conformation.Conformation: current variant for 412 CYS\ncore.conformation.Conformation: current variant for 440 CYS\ncore.conformation.Conformation: current variant for 412 CYD\ncore.conformation.Conformation: current variant for 440 CYD\ncore.io.pdb.pdb_writer: [ ERROR ] StructFileRep::dump_pdb: Unable to open file:/outputs/2r0l_all_repack.pdb for writing!!!\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.249657 seconds to load from binary\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definiPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nSequence:\nDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR\n\nSequence:\nDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSIIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR\nCDR\n134\n135\n136\n137\n138\n139\n140\n141\n142\n143\n\nCDR+Neighbors\n96\n109\n110\n111\n112\n130\n131\n132\n133\n134 CDR\n135 CDR\n136 CDR\n137 CDR\n138 CDR\n139 CDR\n140 CDR\n141 CDR\n142 CDR\n143 CDR\n144\n145\n155\n156\n157\n158\n159\n160\n161\n162\n163\n165\n167\n178\n180\n181\n182\n183\n184\n185\n186\n187\n203\n204\n205\n206\n207\n208\n212\n214\n215\n268\n269\n270\n302\n304\n305\n306\n307\n308\n309\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\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\tTRUE\tFALSE\tPRO\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\tTRUE\tFALSE\tGLU:NtermProteinFull\n110\tTRUE\tFALSE\tVAL\n111\tTRUE\tFALSE\tGLN\n112\tTRUE\tFALSE\tLEU\n113\tFALSE\tFALSE\t\n114\tFALSE\tFALSE\t\n115\tFALSE\tFALSE\t\n116\tFALSE\tFALSE\t\n117\tFALSE\tFALSE\t\n118\tFALSE\tFALSE\t\n119\tFALSE\tFALSE\t\n120\tFALSE\tFALSE\t\n121\tFALSE\tFALSE\t\n122\tFALSE\tFALSE\t\n123\tFALSE\tFALSE\t\n124\tFALSE\tFALSE\t\n125\tFALSE\tFALSE\t\n126\tFALSE\tFALSE\t\n127\tFALSE\tFALSE\t\n128\tFALSE\tFALSE\t\n129\tFALSE\tFALSE\t\n130\tTRUE\tFALSE\tCYS:disulfide\n131\tTRUE\tFALSE\tALA\n132\tTRUE\tFALSE\tALA\n133\tTRUE\tFALSE\tSER\n134\tTRUE\tFALSE\tGLY\n135\tTRUE\tFALSE\tPHE\n136\tTRUE\tFALSE\tTHR\n137\tTRUE\tFALSE\tILE\n138\tTRUE\tFALSE\tSER\n139\tTRUE\tFALSE\tASN\n140\tTRUE\tFALSE\tSER\n141\tTRUE\tFALSE\tGLY\n142\tTRUE\tFALSE\tILE\n143\tTRUE\tFALSE\tHIS,HIS_D\n144\tTRUE\tFALSE\tTRP\n145\tTRUE\tFALSE\tVAL\n146\tFALSE\tFALSE\t\n147\tFALSE\tFALSE\t\n148\tFALSE\tFALSE\t\n149\tFALSE\tFALSE\t\n150\tFALSE\tFALSE\t\n151\tFALSE\tFALSE\t\n152\tFALSE\tFALSE\t\n153\tFALSE\tFALSE\t\n154\tFALSE\tFALSE\t\n155\tTRUE\tFALSE\tTRP\n156\tTRUE\tFALSE\tVAL\n157\tTRUE\tFALSE\tGLY\n158\tTRUE\tFALSE\tTRP\n159\tTRUE\tFALSE\tILE\n160\tTRUE\tFALSE\tTYR\n161\tTRUE\tFALSE\tPRO\n162\tTRUE\tFALSE\tTHR\n163\tTRUE\tFALSE\tGLY\n164\tFALSE\tFALSE\t\n165\tTRUE\tFALSE\tALA\n166\tFALSE\tFALSE\t\n167\tTRUE\tFALSE\tASP\n168\tFALSE\tFALSE\t\n169\tFALSE\tFALSE\t\n170\tFALSE\tFALSE\t\n171\tFALSE\tFALSE\t\n172\tFALSE\tFALSE\t\n173\tFALSE\tFALSE\t\n174\tFALSE\tFALSE\t\n175\tFALSE\tFALSE\t\n176\tFALSE\tFALSE\t\n177\tFALSE\tFALSE\t\n178\tTRUE\tFALSE\tILE\n179\tFALSE\tFALSE\t\n180\tTRUE\tFALSE\tALA\n181\tTRUE\tFALSE\tASP\n182\tTRUE\tFALSE\tTHR\n183\tTRUE\tFALSE\tSER\n184\tTRUE\tFALSE\tLYS\n185\tTRUE\tFALSE\tASN\n186\tTRUE\tFALSE\tTHR\n187\tTRUE\tFALSE\tALA\n188\tFALSE\tFALSE\t\n189\tFALSE\tFALSE\t\n190\tFALSE\tFALSE\t\n191\tFALSE\tFALSE\t\n192\tFALSE\tFALSE\t\n193\tFALSE\tFALSE\t\n194\tFALSE\tFALSE\t\n195\tFALSE\tFALSE\t\n196\tFALSE\tFALSE\t\n197\tFALSE\tFALSE\t\n198\tFALSE\tFALSE\t\n199\tFALSE\tFALSE\t\n200\tFALSE\tFALSE\t\n201\tFALSE\tFALSE\t\n202\tFALSE\tFALSE\t\n203\tTRUE\tFALSE\tTYR\n204\tTRUE\tFALSE\tCYS:disulfide\n205\tTRUE\tFALSE\tALA\n206\tTRUE\tFALSE\tARG\n207\tTRUE\tFALSE\tPHE\n208\tTRUE\tFALSE\tTRP\n209\tFALSE\tFALSE\t\n210\tFALSE\tFALSE\t\n211\tFALSE\tFALSE\t\n212\tTRUE\tFALSE\tPHE\n213\tFALSE\tFALSE\t\n214\tTRUE\tFALSE\tTYR\n215\tTRUE\tFALSE\tTRP\n216\tFALSE\tFALSE\t\n217\tFALSE\tFALSE\t\n218\tFALSE\tFALSE\t\n219\tFALSE\tFALSE\t\n220\tFALSE\tFALSE\t\n221\tFALSE\tFALSE\t\n222\tFALSE\tFALSE\t\n223\tFALSE\tFALSE\t\n224\tFALSE\tFALSE\t\n225\tFALSE\tFALSE\t\n226\tFALSE\tFALSE\t\n227\tFALSE\tFALSE\t\n228\tFALSE\tFALSE\t\n229\tFALSE\tFALSE\t\n230\tFALSE\tFALSE\t\n231\tFALSE\tFALSE\t\n232\tFALSE\tFALSE\t\n233\tFALSE\tFALSE\t\n234\tFALSE\tFALSE\t\n23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read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\ncore.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] ################ Cloning pose and building neighbor graph ################\ncore.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] Ensure that pose is either scored or has update_residue_neighbors() called\ncore.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] before using NeighborhoodResidueSelector for maximum performance!\ncore.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] ##########################################################################\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster fo\n#Packer_Task\n\nThreads to request: ALL 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LSE\t\n434\tFALSE\tFALSE\t\n435\tFALSE\tFALSE\t\n436\tFALSE\tFALSE\t\n437\tFALSE\tFALSE\t\n438\tFALSE\tFALSE\t\n439\tFALSE\tFALSE\t\n440\tFALSE\tFALSE\t\n441\tFALSE\tFALSE\t\n442\tFALSE\tFALSE\t\n443\tFALSE\tFALSE\t\n444\tFALSE\tFALSE\t\n445\tFALSE\tFALSE\t\n446\tFALSE\tFALSE\t\n447\tFALSE\tFALSE\t\n448\tFALSE\tFALSE\t\n449\tFALSE\tFALSE\t\n450\tFALSE\tFALSE\t\n451\tFALSE\tFALSE\t\n452\tFALSE\tFALSE\t\n453\tFALSE\tFALSE\t\n454\tFALSE\tFALSE\t\n455\tFALSE\tFALSE\t\n456\tFALSE\tFALSE\t\n457\tFALSE\tFALSE\t\n458\tFALSE\tFALSE\t\n459\tFALSE\tFALSE\t\n460\tFALSE\tFALSE\t\n461\tFALSE\tFALSE\t\n462\tFALSE\tFALSE\t\n463\tFALSE\tFALSE\t\n464\tFALSE\tFALSE\t\nr H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.040\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.051\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.265\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.559\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.581\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: \nrelaxed -520.74221059479\noriginal -520.74221059479\ndelta 0.0\nSetting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\ncore.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\ncore.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\ncore.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors.\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\nprotocols.loops.loops_main: Added cutpoint variant to residue 138\nprotocols.loops.loops_main: Added cutpoint variant to residue 139\n[NbConvertApp] Converting notebook 06.02-Packing-design-and-regional-relax.ipynb to python\n[NbConvertApp] Writing 19287 bytes to 06.02-Packing-design-and-regional-relax.py\n/bin/sh: 1: pip: not found\n06.02-Packing-design-and-regional-relax.py:42: 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.kinematics import MoveMap\n", "state": "passed"}, "06.03-Design-with-a-resfile-and-relax": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.03-Design-with-a-resfile-and-relax.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.03-Design-with-a-resfile-and-relax.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1891472742 seed_offset=0 real_seed=-1891472742\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1891472742 RG_type=mt19937\nNATAA\nstart\n3 A ALLAAxc\n4 A ALLAAxc\n16 A ALLAAxc\n26 A ALLAAxc\n32 A ALLAAxc\n40 A ALLAAxc\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ignore_unrecognized_res 1 -ex1 -ex2aro -detect_disulf 0 -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-208888591 seed_offset=0 real_seed=-208888591\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-208888591 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.75134 seconds.\ncore.import_pose.import_pose: File '1AB1.clean.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1 in file 1AB1.clean.pdb. Best match rsd_type: THR:NtermProteinFull\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.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\ncore.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\ncore.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors.\ncore.pack.task: Packer task: initialize from command line() \nprotocols.DsspMover: LEELLLHHHHHHHHHHHLLLLLHHHHHHHHLLEELLLLLLLLLLLL\nprotocols.fold_from_loops.DisplayPoseLabelsMover: SEQUENCE TTCCPSIVARSNFNVCRLPGTSEAICATYTGCIIIPGATCPGDYAN\nprotocols.fold_from_loops.DisplayPoseLabelsMover: STRUCTURE LEELLLHHHHHHHHHHHLLLLLHHHHHHHHLLEELLLLLLLLLLLL\nprotocols.fold_from_loops.DisplayPoseLabelsMover: MVMP_BB **********************************************\nprotocols.fold_from_loops.DisplayPoseLabelsMover: MVMP_CHI **********************************************\ncore.pack.task: Packer task: initialize from command line() \nprotocols.fold_from_loops.DisplayPoseLabelsMover: DESIGN --**-----------*---------*-----*-------*------\nprotocols.fold_from_loops.DisplayPoseLabelsMover: REPACK **********************************************\nprotocols.fold_from_loops.DisplayPoseLabelsMover: FOLDTREE *********************************************C\nprotocols.fold_from_loops.DisplayPoseLabelsMover: \nprotocols.fold_from_loops.DisplayPoseLabelsMover: FOLD_TREE EDGE 1 46 -1 \nprotocols.fold_from_loops.DisplayPoseLabelsMover: T[THR:NtermProteinFull]TCCPSIVARSNFNVCRLPGTSEAICATYTGCIIIPGATCPGDYAN[ASN:CtermProteinFull]\nprotocols.fold_from_loops.DisplayPoseLabelsMover: PDB file name: 1AB1.clean.pdb\nprotocols.fold_from_loops.DisplayPoseLabelsMover: Pose Range Chain PDB Range | #Residues #Atoms\n\nprotocols.fold_from_loops.DisplayPoseLabelsMover: 0001 -- 0046 A 0001 -- 0046 | 0046 residues; 00649 atoms\nprotocols.fold_from_loops.DisplayPoseLabelsMover: TOTAL | 0046 residues; 00649 atoms\nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\nprotocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.040\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.051\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.265\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.559\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.581\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\ncore.energy_methods.CartesianBondedEnergy: Creating new peptide-bonded energy container (46)\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.358883 seconds to load from binarPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n[3, 4, 16, 26, 32, 40]\nPDB file name: 1AB1.clean.pdb\n Pose Range Chain PDB Range | #Residues #Atoms\n\n0001 -- 0046 A 0001 -- 0046 | 0046 residues; 00649 atoms\n TOTAL | 0046 residues; 00649 atoms\n\nmap_unsigned_long_char{1: A}\nA\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tTHR:NtermProteinFull\n2\tTRUE\tFALSE\tTHR\n3\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n4\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n5\tTRUE\tFALSE\tPRO\n6\tTRUE\tFALSE\tSER\n7\tTRUE\tFALSE\tILE\n8\tTRUE\tFALSE\tVAL\n9\tTRUE\tFALSE\tALA\n10\tTRUE\tFALSE\tARG\n11\tTRUE\tFALSE\tSER\n12\tTRUE\tFALSE\tASN\n13\tTRUE\tFALSE\tPHE\n14\tTRUE\tFALSE\tASN\n15\tTRUE\tFALSE\tVAL\n16\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n17\tTRUE\tFALSE\tARG\n18\tTRUE\tFALSE\tLEU\n19\tTRUE\tFALSE\tPRO\n20\tTRUE\tFALSE\tGLY\n21\tTRUE\tFALSE\tTHR\n22\tTRUE\tFALSE\tSER\n23\tTRUE\tFALSE\tGLU\n24\tTRUE\tFALSE\tALA\n25\tTRUE\tFALSE\tILE\n26\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n27\tTRUE\tFALSE\tALA\n28\tTRUE\tFALSE\tTHR\n29\tTRUE\tFALSE\tTYR\n30\tTRUE\tFALSE\tTHR\n31\tTRUE\tFALSE\tGLY\n32\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n33\tTRUE\tFALSE\tILE\n34\tTRUE\tFALSE\tILE\n35\tTRUE\tFALSE\tILE\n36\tTRUE\tFALSE\tPRO\n37\tTRUE\tFALSE\tGLY\n38\tTRUE\tFALSE\tALA\n39\tTRUE\tFALSE\tTHR\n40\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n41\tTRUE\tFALSE\tPRO\n42\tTRUE\tFALSE\tGLY\n43\tTRUE\tFALSE\tASP\n44\tTRUE\tFALSE\tTYR\n45\tTRUE\tFALSE\tALA\n46\tTRUE\tFALSE\tASN:CtermProteinFull\n\nCPU times: user 1min 30s, sys: 293 ms, total: 1min 30s\nWall time: 1min 30s\n-2389.9257930271992\nThe delta total_score for residue 3 between start_pose and pose is -12.306852938568152\nThe delta total_score for residue 4 between start_pose and pose is -164.62136422558848\nThe delta total_score for residue 16 between start_pose and pose is -204.3193352944384\nThe delta total_score for residue 26 between start_pose and pose is -7.718284914586133\nThe delta total_score for residue 32 between start_pose and pose is -7.132142829210039\nThe delta total_score for residue 40 between start_pose and pose is -6.162817444442856\ny\nprotocols.relax.FastRelax: CMD: repeat 2280.6 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2280.6 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1412.02 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 5671 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack 73.9562 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 81.2425 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min -175.484 0.656597 0.656597 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight -175.484 0.656597 0.656597 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep -82.0303 0.656597 0.656597 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 3587 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack -95.3575 0.656597 0.656597 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep -91.8843 0.656597 0.656597 0.154\nprotocols.relax.FastRelax: CMD: min -138.767 0.645861 0.645861 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight -138.767 0.645861 0.645861 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep -117.147 0.645861 0.645861 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 3491 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack -117.147 0.645861 0.645861 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep -115.443 0.645861 0.645861 0.31955\nprotocols.relax.FastRelax: CMD: min -123.199 0.639186 0.639186 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight -123.199 0.639186 0.639186 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep -105.666 0.639186 0.639186 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 3443 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack -105.666 0.639186 0.639186 0.55\nprotocols.relax.FastRelax: CMD: min -109.323 0.636339 0.636339 0.55\nprotocols.relax.FastRelax: MRP: 0 -109.323 -109.323 0.636339 0.636339 \nprotocols.relax.FastRelax: CMD: accept_to_best -109.323 0.636339 0.636339 0.55\nprotocols.relax.FastRelax: CMD: endrepeat -109.323 0.636339 0.636339 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\ncore.energy_methods.CartesianBondedEnergy: Creating new peptide-bonded energy container (46)\n[NbConvertApp] Converting notebook 06.03-Design-with-a-resfile-and-relax.ipynb to python\n[NbConvertApp] Writing 10910 bytes to 06.03-Design-with-a-resfile-and-relax.py\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n", "state": "passed"}, "06.04-Protein-Design-2": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.04-Protein-Design-2.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.04-Protein-Design-2.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1378343188 seed_offset=0 real_seed=1378343188\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1378343188 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ignore_unrecognized_res 1 -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1087056799 seed_offset=0 real_seed=-1087056799\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1087056799 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.8308 seconds.\ncore.import_pose.import_pose: File '1AB1.clean.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1 in file 1AB1.clean.pdb. Best match rsd_type: THR:NtermProteinFull\ncore.conformation.Conformation: Found disulfide between residues 3 40\ncore.conformation.Conformation: current variant for 3 CYS\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 3 CYD\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: Found disulfide between residues 4 32\ncore.conformation.Conformation: current variant for 4 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 4 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 16 26\ncore.conformation.Conformation: current variant for 16 CYS\ncore.conformation.Conformation: current variant for 26 CYS\ncore.conformation.Conformation: current variant for 16 CYD\ncore.conformation.Conformation: current variant for 26 CYD\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.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\ncore.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\ncore.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors.\ncore.pack.task: Packer task: initialize from command line() \nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\nprotocols.relax.RelaxScriptManager: Looking for MonomerDesign2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/MonomerDesign2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.059\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.092\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.323\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.568\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.633\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\ncore.energy_methods.CartesianBondedEnergy: Creating new peptide-bonded energy container (46)\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.362169 seconds to load from binary\nprotocols.relax.FastRelax: CMD: repeat 2280.6 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2280.6 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1429.21 0 0 0.03245\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 5220 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack 82.5747 0 0 0.03245\nprotocols.relax.FastRelax: CMD: scale:fa_rep 89.8787 0 0 0.0506\nprotocols.relax.FastRelax: CMD: min -162.512 0.981158 0.981158 0.0506\nprotocols.relax.FastRelax: CMD: coord_cst_weight -162.512 0.981158 0.981158 0.0506\nproPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nvector1_unsigned_long[3, 4, 16, 26, 32, 40]\nvector1_unsigned_long[3, 4, 16, 26, 32, 40]\nPDB file name: 1AB1.clean.pdb\n Pose Range Chain PDB Range | #Residues #Atoms\n\n0001 -- 0046 A 0001 -- 0046 | 0046 residues; 00649 atoms\n TOTAL | 0046 residues; 00649 atoms\n\nvector1_unsigned_long[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]\nvector1_unsigned_long[3, 4, 16, 26, 32, 40]\nvector1_unsigned_long[1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tTHR:NtermProteinFull\n2\tTRUE\tFALSE\tTHR\n3\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n4\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n5\tTRUE\tFALSE\tPRO\n6\tTRUE\tFALSE\tSER\n7\tTRUE\tFALSE\tILE\n8\tTRUE\tFALSE\tVAL\n9\tTRUE\tFALSE\tALA\n10\tTRUE\tFALSE\tARG\n11\tTRUE\tFALSE\tSER\n12\tTRUE\tFALSE\tASN\n13\tTRUE\tFALSE\tPHE\n14\tTRUE\tFALSE\tASN\n15\tTRUE\tFALSE\tVAL\n16\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n17\tTRUE\tFALSE\tARG\n18\tTRUE\tFALSE\tLEU\n19\tTRUE\tFALSE\tPRO\n20\tTRUE\tFALSE\tGLY\n21\tTRUE\tFALSE\tTHR\n22\tTRUE\tFALSE\tSER\n23\tTRUE\tFALSE\tGLU\n24\tTRUE\tFALSE\tALA\n25\tTRUE\tFALSE\tILE\n26\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n27\tTRUE\tFALSE\tALA\n28\tTRUE\tFALSE\tTHR\n29\tTRUE\tFALSE\tTYR\n30\tTRUE\tFALSE\tTHR\n31\tTRUE\tFALSE\tGLY\n32\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n33\tTRUE\tFALSE\tILE\n34\tTRUE\tFALSE\tILE\n35\tTRUE\tFALSE\tILE\n36\tTRUE\tFALSE\tPRO\n37\tTRUE\tFALSE\tGLY\n38\tTRUE\tFALSE\tALA\n39\tTRUE\tFALSE\tTHR\n40\tTRUE\tTRUE\tALA,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n41\tTRUE\tFALSE\tPRO\n42\tTRUE\tFALSE\tGLY\n43\tTRUE\tFALSE\tASP\n44\tTRUE\tFALSE\tTYR\n45\tTRUE\tFALSE\tALA\n46\tTRUE\tFALSE\tASN:CtermProteinFull\n\nCPU times: user 1min 3s, sys: 375 ms, total: 1min 3s\nWall time: 1min 3s\ntocols.relax.FastRelax: CMD: scale:fa_rep -117.055 0.981158 0.981158 0.154\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 945 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack -117.859 0.981158 0.981158 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep -107.712 0.981158 0.981158 0.17765\nprotocols.relax.FastRelax: CMD: min -136.455 0.845789 0.845789 0.17765\nprotocols.relax.FastRelax: CMD: coord_cst_weight -136.455 0.845789 0.845789 0.17765\nprotocols.relax.FastRelax: CMD: scale:fa_rep -117.859 0.845789 0.845789 0.3124\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 882 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack -117.859 0.845789 0.845789 0.3124\nprotocols.relax.FastRelax: CMD: scale:fa_rep -112.925 0.845789 0.845789 0.34815\nprotocols.relax.FastRelax: CMD: min -119.292 0.766319 0.766319 0.34815\nprotocols.relax.FastRelax: CMD: coord_cst_weight -119.292 0.766319 0.766319 0.34815\nprotocols.relax.FastRelax: CMD: scale:fa_rep -103.776 0.766319 0.766319 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 804 rotamers at 46 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.relax.FastRelax: CMD: repack -103.776 0.766319 0.766319 0.55\nprotocols.relax.FastRelax: CMD: min -107.407 0.620504 0.620504 0.55\nprotocols.relax.FastRelax: MRP: 0 -107.407 -107.407 0.620504 0.620504 \nprotocols.relax.FastRelax: CMD: accept_to_best -107.407 0.620504 0.620504 0.55\nprotocols.relax.FastRelax: CMD: endrepeat -107.407 0.620504 0.620504 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\n[NbConvertApp] Converting notebook 06.04-Protein-Design-2.ipynb to python\n[NbConvertApp] Writing 10485 bytes to 06.04-Protein-Design-2.py\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n", "state": "passed"}, "06.05-HBNet-Before-Design": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.05-HBNet-Before-Design.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.05-HBNet-Before-Design.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1802166720 seed_offset=0 real_seed=-1802166720\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1802166720 RG_type=mt19937\n[ WARNING ] Resetting the global tracer options, which have already been set.\n[ WARNING ] This will not affect Tracers which are already initialized.\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -mute core -mute basic -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1671993446 seed_offset=0 real_seed=-1671993446\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1671993446 RG_type=mt19937\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<MOVERS>\n\t\t<HBNetStapleInterface monte_carlo=\"true\" name=\"hbnet\" store_network_scores_in_pose=\"true\"/>\n\t</MOVERS>\n\t<PROTOCOLS/>\n</ROSETTASCRIPTS>\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"hbnet\" of type HBNetStapleInterface\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\nprotocols.hbnet.HBNet: Creating packer task based on specified task operations...\nprotocols.hbnet.HBNet: Creating packer task based on specified task operations...\nprotocols.hbnet.HBNet: built 9732 rotamers at 84 positions.\nprotocols.hbnet.HBNet: IG: 1544332 bytes\nprotocols.hbnet.HBNet: ==================================================================\nprotocols.hbnet.HBNet: ============ PERFORMING H-BOND NETWORK DESIGN ============\nprotocols.hbnet.HBNet: ==================================================================\nprotocols.hbnet.HBNet: starting monte carlo branching protocol\nprotocols.hbnet.HBNet: \t10% done with branching\nprotocols.hbnet.HBNet: \t20% done with branching\nprotocols.hbnet.HBNet: \t30% done with branching\nprotocols.hbnet.HBNet: \t40% done with branching\nprotocols.hbnet.HBNet: \t50% done with branching\nprotocols.hbnet.HBNet: \t60% done with branching\nprotocols.hbnet.HBNet: \t70% done with branching\nprotocols.hbnet.HBNet: \t80% done with branching\nprotocols.hbnet.HBNet: \t90% done with branching\nprotocols.hbnet.HBNet: \t100% done with branching\nprotocols.hbnet.HBNet: Monte carlo branching protocol found 214 networks.\nprotocols.hbnet.HBNet: NUMBER OF H-BOND NETWORKS AFTER BRANCH: 162\nprotocols.hbnet.HBNet: NUMBER OF NETWORKS AFTER REMOVE REPLICATES = 162\nprotocols.hbnet.HBNet: NUMBER OF NETWORKS AFTER SELECTION = 10\nprotocols.hbnet.HBNet: NUMBER OF NETWORKS AFTER REMOVE_REP = 10\nprotocols.hbnet.HBNet: Designed these new networks that meet your criteria: \nprotocols.hbnet.HBNet: \t#HBNet_rank \t residues \t size \t score \t num_hbonds \t percent_hbond_capacity \t num_unsat_Hpol \tinterf_hbs \t\nprotocols.hbnet.HBNet: \t#network_1\tD_Y_155,D_R_180,D_E_185,D_R_187,E_R_207,backbone\t5\t-0.650077\t8\t0.714286\t0\t3\t\nprotocols.hbnet.HBNet: \t#network_2\tD_Y_155,D_E_185,D_R_187,E_R_207,backbone\t4\t-1.07079\t6\t0.6875\t0\t3\t\nprotocols.hbnet.HBNet: \t#network_3\tD_Y_155,D_R_180,D_E_185,E_R_207\t4\t-0.746147\t5\t0.625\t0\t3\t\nprotocols.hbnet.HBNet: \t#network_4\tD_R_40,D_H_50,D_E_116,E_R_107\t4\t0.153613\t5\t0.625\t0\t2\t\nprotocols.hbnet.HBNet: \t#network_5\tD_R_40,D_E_44,D_H_50,D_E_116,E_R_107\t5\t-0.508065\t6\t0.6\t0\t2\t\nprotocols.hbnet.HBNet: \t#network_6\tD_R_40,D_E_116,E_R_107\t3\t-0.906424\t4\t0.571429\t0\t2\t\nprotocols.hbnet.HBNet: \t#network_7\tD_H_116,E_S_40,E_R_107\t3\t2.36078\t3\t0.555556\t0\t1\t\nprotocols.hbnet.HBNet: \t#network_8\tD_Y_155,D_E_185,E_R_207\t3\t-0.555068\t3\t0.545455\t0\t3\t\nprotocols.hbnet.HBNet: \t#network_9\tD_Q_40,D_H_116,E_S_40,E_R_107\t4\t4.60542\t4\t0.538462\t0\t1\t\nprotocols.hbnet.HBNet: \tPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ninit complete\nsetup complete\nNum residues: 454\nNum packable residues: 116\nNum designable residues: 53\nChange in score 1209.2785780113772\nNum HBNet Residues 5\nChange in score 155.20583159760645\nHBNet_NumUnsatHpol 0.0\nHBNet_Saturation 0.7142857313156128\nHBNet_Score -0.6500769853591919\n#network_10\tD_Q_40,D_N_42,D_H_116,E_S_40,E_R_107\t5\t3.45032\t5\t0.529412\t0\t1\t\nprotocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... \nprotocols.hbnet.HBNet: \n[NbConvertApp] Converting notebook 06.05-HBNet-Before-Design.ipynb to python\n[NbConvertApp] Writing 14156 bytes to 06.05-HBNet-Before-Design.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "06.06-Introduction-to-Parametric-backbone-design": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.06-Introduction-to-Parametric-backbone-design.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.06-Introduction-to-Parametric-backbone-design.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=2000600372 seed_offset=0 real_seed=2000600372\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=2000600372 RG_type=mt19937\n[ WARNING ] Resetting the global tracer options, which have already been set.\n[ WARNING ] This will not affect Tracers which are already initialized.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.0\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.03490658503988659\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.06981317007977318\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.10471975511965978\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.13962634015954636\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.17453292519943295\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.20943951023931956\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.24434609527920614\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.2792526803190927\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.3141592653589793\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.3490658503988659\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.3839724354387525\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.4188790204786391\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.4537856055185257\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.4886921905584123\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\n\n <SCOREFXNS>\n <ScoreFunction name=\"sfxn1\" weights=\"ref2015\"/>\n </SCOREFXNS>\n <MOVERS>\n <MakeBundle name=\"bgs1\"\n helix_length=\"20\"\n r0=\"5\"\n omega0=\"0.5235987755982988\"\n delta_omega0=\"0\"\n delta_omega1=\"0\"\n delta_t=\"0\">\n <Helix/>\n <Helix delta_omega0=\"3.14\" r0_copies_helix=\"1\"/>\n \n </MakeBundle>\n </MOVERS>\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -mute all -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-472520610 seed_offset=0 real_seed=-472520610\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-472520610 RG_type=mt19937\n[NbConvertApp] Converting notebook 06.06-Introduction-to-Parametric-backbone-design.ipynb to python\n[NbConvertApp] Writing 11177 bytes to 06.06-Introduction-to-Parametric-backbone-design.py\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n", "state": "passed"}, "06.07-Introduction-to-DeNovo-protein-design": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.07-Introduction-to-DeNovo-protein-design.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.07-Introduction-to-DeNovo-protein-design.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1678120803 seed_offset=0 real_seed=1678120803\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1678120803 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.91006 seconds.\ncore.import_pose.import_pose: File 'inputs/5J0J.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 70\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 139\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 210\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.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\ncore.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\ncore.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors.\ncore.energy_methods.CartesianBondedEnergy: Creating new peptide-bonded energy container (210)\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.324514 seconds to load from binary\nbasic.io.database: Database file opened: scoring/score_functions/aa_repeat_energy/default_repeat_penalty_table.rpt_pen\nprotocols.constraint_generator.AddConstraints: Adding 843 constraints generated by ConstraintGenerator named contrain_all_backbone_atoms!\nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\nprotocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.040\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.051\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.265\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.559\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.581\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\nprotocols.constraint_generator.RemoveConstraints: Removing 843 constraints from pose generated by contrain_all_backbone_atoms!\nprotocols.grafting.util: Returning 70 residues from 1 to 70\nprotocols.pose_creation.MakePolyXMover: Pose is converted to poly ALA\nprotocols.grafting.util: Returning 139 residues from 71 to 209\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.simple_moves.SwitchChainOrderMover: Number of chains in pose: 2\nprotocols.simple_moves.SwitchChainOrderMover: Now at chain: 1\nprotocols.simple_moves.SwitchChainOrderMover: Now at chain: 2\nprotocols.simple_moves.SwitchChainOrderMover: New pose's foldtree FOLD_TREE EDGE 1 70 -1 EDGE 1 71 1 EDGE 71 209 -1 \nprotocols.constraint_generator.AddConstraints: Adding 838 constraints generated by ConstraintGenerator named contrain_all_backbone_atoms!\nprotocols.aa_composition.AddCompositionConstraintMover: Initialized AACompositionConstraint object from file contents:\n\nPENALTY_DEFINITION\nOR_PROPERTIES AROMATIC ALIPHATIC\nNOT_TYPE LEU\nFRACT_DELTA_START -0.05\nFRACT_DELTA_END 0.05\nPENALTIES 1 0 1 # The above two lines mean that if we're 5% below or 5% above the desired content, we get a 1-point penalty.\nFRACTION 0.4 # Forty percent aromatic or aliphatic, but not leucine\nBEFORE_FUNCTION CONSTANT\nAFTER_FUNCTION CONSTANT\nEND_PENALTY_DEFINITION\n\nPENALTY_DEFINITION\nTYPE LEU\nDELTA_START -1\nDELTA_END 1\nPENALTIES 1 0 1\nFRACTION 0.05 # Five percent leucine\nBEFORE_FUNCTION CONSTANT\nAFTER_FUNCTION CONSTANT\nEND_PENALTY_DEFINITION\n\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: Applying sequence constraints for helix 1, running from residue 2 through residue 32.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding N-terminal sequence constraints to helix.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding C-terminal sequence constraints to helix.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding sequence constraints to helix penalizing helix-disfavouring residue types.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding sequence constraints to helix to control fractional alanine content.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding sequence constraints to helix to enforce a minimum hydrophobic content.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: Applying sequence constraints for helix 2, running from residue 40 through residue 69.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding N-terminal sequence constraints to helix.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding C-terminal sequence constraints to helix.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding sequence constraints to helix penalizing helix-disfavouring residue types.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding sequence constraints to helix to control fractional alanine content.\nprotocols.aa_composition.AddHelixSequenceConstraintsMover: \tAdding sequence constraints to helix to enforce a minimum hydrophobic content.\nprotocols.aa_composition.AddNetChargeConstraintMover: Initialized NetChargeConstraint object from file contents:\n\nDESIRED_CHARGE 0 #Desired net charge is zero.\nPENALTIES_CHARGE_RANGE -1 1 #Penalties are listed in the observed net charge range of -1 to +1.\nPENALTIES 1 0 1 #The penalties are 1 for an observed charge of -1, 0 for an observed charge of 0, and 1 for an observed charge of +1.\nBEFORE_FUNCTION QUADRATIC #Ramp quadratically for observed net charges of -2 or less.\nAFTER_FUNCTION QUADRATIC #Ramp quadratically for observed net charges of +2 or greater.\n\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<RESIDUE_SELECTORS>\n\t\t<Layer name=\"surface\" select_boundary=\"false\" select_core=\"false\" select_surface=\"true\" use_sidechain_neighbors=\"true\"/>\n\t\t<Layer name=\"boundary\" select_boundary=\"true\" select_core=\"false\" select_surface=\"false\" use_sidechain_neighbors=\"true\"/>\n\t\t<Layer name=\"core\" select_boundary=\"false\" select_core=\"true\" select_surface=\"false\" use_sidechain_neighbors=\"true\"/>\n\t\t<SecondaryStructure include_terminal_loops=\"false\" minE=\"2\" minH=\"3\" name=\"sheet\" overlap=\"0\" ss=\"E\" use_dssp=\"true\"/>\n\t\t<SecondaryStructure include_terminal_loops=\"true\" minE=\"2\" minH=\"3\" name=\"entire_loop\" overlap=\"0\" ss=\"L\" use_dssp=\"true\"/>\n\t\t<SecondaryStructure include_terminal_loops=\"false\" minE=\"2\" minH=\"3\" name=\"entire_helix\" overlap=\"0\" ss=\"H\" use_dssp=\"true\"/>\n\t\t<And name=\"helix_cap\" selectors=\"entire_loop\">\n\t\t\t<PrimarySequenceNeighborhood lower=\"1\" selector=\"entire_helix\" upper=\"0\"/>\n\t\t</And>\n\t\t<And name=\"helix_start\" selectors=\"entire_helix\">\n\t\t\t<PrimarySequenceNeighborhood lower=\"0\" selector=\"helix_cap\" upper=\"1\"/>\n\t\t</And>\n\t\t<And name=\"helix\" selectors=\"entire_helix\">\n\t\t\t<Not selector=\"helix_start\"/>\n\t\t</And>\n\t\t<And name=\"loop\" selectors=\"entire_loop\">\n\t\t\t<Not selector=\"helix_cap\"/>\n\t\t</And>\n\t</RESIDUE_SELECTORS>\n\t<TASKOPERATIONS>\n\t\t<DesignRestrictions name=\"layer_design\">\n\t\t\t<Action aas=\"EHKPQR\" selector_logic=\"surface AND helix_start\"/>\n\t\t\t<Action aas=\"EHKQR\" selector_logic=\"surface AND helix\"/>\n\t\t\t<Action aas=\"DEHKNQRST\" selector_logic=\"surface AND sheet\"/>\n\t\t\t<Action aas=\"DEGHKNPQRST\" selector_logic=\"surface AND loop\"/>\n\t\t\t<Action aas=\"ADEIKLMNPQRSTVWY\" selector_logic=\"boundary AND helix_start\"/>\n\t\t\t<Action aas=\"ADEIKLMNQRSTVWY\" selector_logic=\"boundary AND helix\"/>\n\t\t\t<Action aas=\"DEFIKLNQRSTVWY\" selector_logic=\"boundary AND sheet\"/>\n\t\t\t<Action aas=\"ADEFGIKLMNPQRSTVWY\" selector_logic=\"boundary AND loop\"/>\n\t\t\t<Action aas=\"AFILMPVWY\" selector_logic=\"core AND helix_start\"/>\n\t\t\t<Action aas=\"AFILMVWY\" selector_logic=\"core AND helix\"/>\n\t\t\t<Action aas=\"FILVWY\" selector_logic=\"core AND sheet\"/>\n\t\t\t<Action aas=\"AFGILMPVWY\" selector_logic=\"core AND loop\"/>\n\t\t\t<Action aas=\"DNST\" selector_logic=\"helix_cap\"/>\n\t\t</DesignRestrictions>\n\t</TASKOPERATIONS>\n\t<PROTOCOLS/>\n</ROSETTASCRIPTS>\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/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.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting core=false boundary=false surface=true in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting core=false boundary=true surface=false in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting core=true boundary=false surface=false in LayerSelector.\ncore.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial.\ncore.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.\ncore.select.residue_selecPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\nThe starting pose total_score is 3822.9501587800064\nThe starting pose total_score is 24725.950158780008\nPDB file name: \n Pose Range Chain PDB Range | #Residues #Atoms\n\n0001 -- 0070 A 0001 -- 0070 | 0070 residues; 00703 atoms\n0071 -- 0139 B 0071 -- 0139 | 0069 residues; 01187 atoms\n0140 -- 0209 C 0140 -- 0209 | 0070 residues; 01212 atoms\n TOTAL | 0209 residues; 03102 atoms\n\nNow the number of chains = 3\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\rtor.PrimarySequenceNeighborhoodSelector: Using residue selector entire_helix\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: Using residue selector helix_cap\nprotocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named \"layer_design\" of type DesignRestrictions\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\ncore.pack.task: Packer task: initialize from command line() \ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\nprotocols.DsspMover: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\nprotocols.fold_from_loops.DisplayPoseLabelsMover: SEQUENCE AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAYKIKETLKRLEDSLRELRRILEELKEMLERLEKNPDKDVIVEVLKVIVKAIEASVENQRISAENQKALATKYKIKETLKRLEDSLRELRRILEELKEMLERLEKNPDKDVIVEVLKVIVKAIEASVENQRISAENQKALX\nprotocols.fold_from_loops.DisplayPoseLabelsMover: STRUCTURE LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\nprotocols.fold_from_loops.DisplayPoseLabelsMover: MVMP_BB ..................................................................................................................................................................................................................\nprotocols.fold_from_loops.DisplayPoseLabelsMover: MVMP_CHI **********************************************************************..*...*..*...*..**..*..**..*..*...*....*..*...*..*..**..*...*..*..**.......................................*..**..**.**..**.**..**.**..**.**\ncore.pack.task: Packer task: initialize from command line() \ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLL\ncore.select.residue_selector.PrimarySequenceNeighborhoodSelector: ]\nprotocols.fold_from_loops.DisplayPoseLabelsMover: DESIGN **********************************************************************--------------------------------------------------------------------------------------------------------------------------------------------\nprotocols.fold_from_loops.DisplayPoseLabelsMover: REPACK **********************************************************************------*--*---*--**--*--**--*--*---*----*--*---*--*--*-------*-----**------------------------------------------**--**-**--**--*---*-**---*-**\nprotocols.fold_from_loops.DisplayPoseLabelsMover: FOLDTREE 1********************************************************************C1****************************************************2************************************************************************************C2/C\nprotocols.fold_from_loops.DisplayPoseLabelsMover: \nprotocols.fold_from_loops.DisplayPoseLabelsMover: FOLD_TREE EDGE 210 124 2 EDGE 124 71 -1 EDGE 124 209 -1 EDGE 71 1 1 EDGE 1 70 -1 \nprotocols.fold_from_loops.DisplayPoseLabelsMover: A[ALA:NtermProteinFull]AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA[ALA:CtermProteinFull]Y[TYR:NtermProteinFull]KIKETLKRLEDSLRELRRILEELKEMLERLEKNPDKDVIVEVLKVIVKAIEASVENQRISAENQKALA[ALA:CtermProteinFull]T[THR:NtermProteinFull]KYKIKETLKRLEDSLRELRRILEELKEMLERLEKNPDKDVIVEVLKVIVKAIEASVENQRISAENQKALX\nprotocols.fold_from_loops.DisplayPoseLabelsMover: PDB file name: \nprotocols.fold_from_loops.DisplayPoseLabelsMover: Pose Range Chain PDB Range | #Residues #Atoms\n\nprotocols.fold_from_loops.DisplayPoseLabelsMover: 0001 -- 0070 A 0001 -- 0070 | 0070 residues; 00703 atoms\nprotocols.fold_from_loops.DisplayPoseLabelsMover: 0071 -- 0139 B 0071 -- 0139 | 0069 residues; 01187 atoms\nprotocols.fold_from_loops.DisplayPoseLabelsMover: 0140 -- 0209 C 0140 -- 0209 | 0070 residues; 01212 atoms\nprotocols.fold_from_loops.DisplayPoseLabelsMover: 0210 -- 0210 z 0001 -- 0001 | 0001 residues; 00003 atoms\nprotocols.fold_from_loops.DisplayPoseLabelsMover: TOTAL | 0210 residues; 03105 atoms\nprotocols.relax.FastRelax: KillA2019 has been renamed to PolarDesign2019\nprotocols.relax.RelaxScriptManager: score12 : 116.271\nprotocols.relax.RelaxScriptManager: talaris2013 : 109.417\nprotocols.relax.RelaxScriptManager: talaris2014 : 109.347\nprotocols.relax.RelaxScriptManager: ref2015 : 106.875\nprotocols.relax.RelaxScriptManager: beta_nov16 : 114.938\nprotocols.relax.RelaxScriptManager: Looking for PolarDesign2019.ref2015.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/PolarDesign2019.ref2015.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: reference -0.511909 2.0282 -3.29233 -3.74112 2.5917 -1.12843 -1.33724 3.25715 -1.56117 2.65488 2.88076 -2.80685 -1.5498 -2.69754 -1.62133 -1.86628 -0.0648395 2.6561 4.7344 1.37564\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.059\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep\u001b[2K\r#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tTRUE\tASP:NtermProteinFull,ASN:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull\n2\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,PRO,GLN,ARG\n3\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n4\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n5\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n6\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n7\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n8\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n9\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n10\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n11\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n12\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n13\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n14\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n15\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n16\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n17\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n18\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n19\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n20\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n21\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n22\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n23\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n24\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n25\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n26\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n27\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n28\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n29\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n30\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n31\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n32\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n33\tTRUE\tTRUE\tASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR\n34\tTRUE\tTRUE\tASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR\n35\tTRUE\tTRUE\tASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR\n36\tTRUE\tTRUE\tASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR\n37\tTRUE\tTRUE\tASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR\n38\tTRUE\tTRUE\tASP,GLU,GLY,HIS,HIS_D,LYS,ASN,PRO,GLN,ARG,SER,THR\n39\tTRUE\tTRUE\tASP,ASN,SER,THR\n40\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n41\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n42\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n43\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n44\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n45\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n46\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n47\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n48\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n49\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n50\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n51\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n52\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n53\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n54\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n55\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n56\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n57\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n58\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n59\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n60\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n61\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n62\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n63\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n64\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n65\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n66\tTRUE\tTRUE\tALA,PHE,ILE,LEU,MET,VAL,TRP,TYR\n67\tTRUE\tTRUE\tGLU,HIS,HIS_D,LYS,GLN,ARG\n68\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n69\tTRUE\tTRUE\tALA,ASP,GLU,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR\n70\tTRUE\tTRUE\tALA:CtermProteinFull,ASP:CtermProteinFull,GLU:CtermProteinFull,PHE:CtermProteinFull,GLY:CtermProteinFull,ILE:CtermProteinFull,LYS:CtermProteinFull,LEU:CtermProteinFull,MET:CtermProteinFull,ASN:CtermProteinFull,PRO:CtermProteinFull,GLN:CtermProteinFull,ARG:CtermProteinFull,SER:CtermProteinFull,THR:CtermProteinFull,VAL:CtermProteinFull,TRP:CtermProteinFull,TYR:CtermProteinFull\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\tTRUE\tFALSE\tLEU\n78\tFALSE\tFALSE\t\n79\tFALSE\tFALSE\t\n80\tTRUE\tFALSE\tLEU\n81\tFALSE\tFALSE\t\n82\tFALSE\tFALSE\t\n83\tFALSE\tFALSE\t\n84\tTRUE\tFALSE\tLEU\n85\tFALSE\tFALSE\t\n86\tFALSE\tFALSE\t\n87\tTRUE\tFALSE\tLEU\n88\tTRUE\tFALSE\tARG\n89\tFALSE\tFALSE\t\n90\tFALSE\tFALSE\t\n91\tTRUE\tFALSE\tLEU\n92\tFALSE\tFALSE\t\n93\tFALSE\tFALSE\t\n94\tTRUE\tFALSE\tLEU\n95\tTRUE\tFALSE\tLYS\n96\tFALSE\tFALSE\t\n97\tFALSE\tFALSE\t\n98\tTRUE\tFALSE\tLEU\n99\tFALSE\tFALSE\t\n100\tFALSE\tFALSE\t\n101\tTRUE\tFALSE\tLEU\n102\tFALSE\tFALSE\t\n103\tFALSE\tFALSE\t\n104\tFALSE\tFALSE\t\n105\tTRUE\tFALSE\tPRO\n106\tFALSE\tFALSE\t\n107\tFALSE\tFALSE\t\n108\tFALSE\tFALSE\t\n109\tFALSE\tFALSE\t\n110\tTRUE\tFALSE\tILE\n111\tFALSE\tFALSE\t\n112\tFALSE\tFALSE\t\n113\tTRUE\tFALSE\tVAL\n114\tFALSE\tFALSE\t\n115\tFALSE\tFALSE\t\n116\tFALSE\tFALSE\t\n117\tTRUE\tFALSE\tILE\n118\tFALSE\tFALSE\t\n119\tFALSE\tFALSE\t\n120\tTRUE\tFALSE\tALA\n121\tFALSE\tFALSE\t\n122\tFALSE\tFALSE\t\n123\tTRUE\tFALSE\tALA\n124\tFALSE\tFALSE\t\n125\tFALSE\tFALSE\t\n126\tFALSE\tFALSE\t\n127\tFALSE\tFALSE\t\n128\tFALSE\tFALSE\t\n129\tFALSE\tFALSE\t\n130\tFALSE\tFALSE\t\n131\tTRUE\tFALSE\tSER\n132\tFALSE\tFALSE\t\n133\tFALSE\tFALSE\t\n134\tFALSE\tFALSE\t\n135\tFALSE\tFALSE\t\n136\tFALSE\tFALSE\t\n137\tTRUE\tFALSE\tALA\n138\tTRUE\tFALSE\tLEU\n139\tFALSE\tFALSE\t\n140\tFALSE\tFALSE\t\n141\tFALSE\tFALSE\t\n142\tFALSE\tFALSE\t\n143\tFALSE\tFALSE\t\n144\tFALSE\tFALSE\t\n145\tFALSE\tFALSE\t\n146\tFALSE\tFALSE\t\n147\tFALSE\tFALSE\t\n148\tFALSE\tFALSE\t\n149\tFALSE\tFALSE\t\n150\tFALSE\tFALSE\t\n151\tFALSE\tFALSE\t\n152\tFALSE\tFALSE\t\n153\tFALSE\tFALSE\t\n154\tFALSE\tFALSE\t\n155\tFALSE\tFALSE\t\n156\tFALSE\tFALSE\t\n157\tFALSE\tFALSE\t\n158\tFALSE\tFALSE\t\n159\tFALSE\tFALSE\t\n160\tFALSE\tFALSE\t\n161\tFALSE\tFALSE\t\n162\tFALSE\tFALSE\t\n163\tFALSE\tFALSE\t\n164\tFALSE\tFALSE\t\n165\tFALSE\tFALSE\t\n166\tFALSE\tFALSE\t\n167\tFALSE\tFALSE\t\n168\tFALSE\tFALSE\t\n169\tFALSE\tFALSE\t\n170\tFALSE\tFALSE\t\n171\tFALSE\tFALSE\t\n172\tFALSE\tFALSE\t\n173\tFALSE\tFALSE\t\n174\tFALSE\tFALSE\t\n175\tFALSE\tFALSE\t\n176\tFALSE\tFALSE\t\n177\tFALSE\tFALSE\t\n178\tFALSE\tFALSE\t\n179\tFALSE\tFALSE\t\n180\tFALSE\tFALSE\t\n181\tTRUE\tFALSE\tILE\n182\tTRUE\tFALSE\tVAL\n183\tFALSE\tFALSE\t\n184\tFALSE\tFALSE\t\n185\tTRUE\tFALSE\tLEU\n186\tTRUE\tFALSE\tLYS\n187\tFALSE\tFALSE\t\n188\tTRUE\tFALSE\tILE\n189\tTRUE\tFALSE\tVAL\n190\tFALSE\tFALSE\t\n191\tFALSE\tFALSE\t\n192\tTRUE\tFALSE\tILE\n193\tTRUE\tFALSE\tGLU\n194\tFALSE\tFALSE\t\n195\tFALSE\tFALSE\t\n196\tTRUE\tFALSE\tVAL\n197\tFALSE\tFALSE\t\n198\tFALSE\tFALSE\t\n199\tFALSE\tFALSE\t\n200\tTRUE\tFALSE\tARG\n201\tFALSE\tFALSE\t\n202\tTRUE\tFALSE\tSER\n203\tTRUE\tFALSE\tALA\n204\tFALSE\tFALSE\t\n205\tFALSE\tFALSE\t\n206\tFALSE\tFALSE\t\n207\tTRUE\tFALSE\tLYS\n208\tFALSE\tFALSE\t\n209\tTRUE\tFALSE\tLEU\n210\tTRUE\tFALSE\tVRT\n\nKYKIKETLKRLEDSLRELRRILEELKEMLERLEKNPDKDVIVEVLKVIVKAIEASVENQRISAENQKALA\nDEHERRIMEERHRMEEKFHHEMERMHRKKHQRHQTTSKSEYEHMFETIMRMMEWFERSFERMQEMYRQRT\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r 0.092\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: reference 0.335091 2.4652 -2.85533 -3.29412 1.6487 -1.27143 -1.07024 2.80415 -1.20417 2.08188 2.06776 -2.26985 -1.5128 -2.21054 -1.15433 -1.25928 0.392161 2.6131 2.9414 0.752641\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.323\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: reference 0.742591 2.7127 -2.62783 -3.12662 1.1962 -0.823929 -0.992739 2.55165 -1.09667 1.83938 1.72526 -2.04235 -1.6253 -2.10304 -1.06683 -0.951779 0.589661 2.6206 2.0389 0.440141\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.568\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.633\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: reset_reference\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\ncore.import_pose.import_pose: File 'expected_outputs/designed_relaxed_pose.pdb' automatically determined to be of type PDB\nprotocols.grafting.util: Returning 70 residues from 1 to 70\nprotocols.simple_filters.NetChargeFilter: AA: -1 ASP 1\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 2\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 4\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 5\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 6\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 9\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 10\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 11\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 13\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 15\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 16\nprotocols.simple_filters.NetChargeFilter: AA: +1 LYS 17\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 21\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 23\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 24\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 27\nprotocols.simple_filters.NetChargeFilter: AA: +1 LYS 28\nprotocols.simple_filters.NetChargeFilter: AA: +1 LYS 29\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 32\nprotocols.simple_filters.NetChargeFilter: AA: +1 LYS 38\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 40\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 42\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 46\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 50\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 53\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 56\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 57\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 60\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 61\nprotocols.simple_filters.NetChargeFilter: AA: -1 GLU 64\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 67\nprotocols.simple_filters.NetChargeFilter: AA: +1 ARG 69\nprotocols.simple_filters.NetChargeFilter: The net charge is: 0\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<SCOREFXNS>\n\t\t<ScoreFunction name=\"fa_default\" weights=\"ref2015\"/>\n\t</SCOREFXNS>\n\t<FILTERS>\n\t\t<BuriedUnsatHbonds confidence=\"0\" cutoff=\"99999\" ignore_bb_heavy_unsats=\"false\" ignore_surface_res=\"true\" name=\"uhb_sc\" print_out_info_to_pdb=\"false\" report_bb_heavy_atom_unsats=\"false\" report_sc_heavy_atom_unsats=\"true\" residue_surface_cutoff=\"20.0\" scorefxn=\"fa_default\" use_hbnet_behavior=\"false\" use_reporter_behavior=\"true\"/>\n\t\t<BuriedUnsatHbonds confidence=\"0\" cutoff=\"99999\" ignore_bb_heavy_unsats=\"false\" ignore_surface_res=\"true\" name=\"uhb_bb\" print_out_info_to_pdb=\"false\" report_bb_heavy_atom_unsats=\"true\" report_sc_heavy_atom_unsats=\"false\" residue_surface_cutoff=\"20.0\" scorefxn=\"fa_default\" use_hbnet_behavior=\"false\" use_reporter_behavior=\"true\"/>\n\t</FILTERS>\n\t<PROTOCOLS/>\n</ROSETTASCRIPTS>\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.jd2.parser.ScoreFunctionLoader: defined score function \"fa_default\" with weights \"ref2015\"\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined filter named \"uhb_sc\" of type BuriedUnsatHbonds\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined filter named \"uhb_bb\" of type BuriedUnsatHbonds\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: USER HAS SPECIFIED CUSTOM REPORTING BEHAVIOR FOR # UNSATS\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nbasic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::recompute\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.simple_filters.BuriedUnsatHbondFilter: buried unsats in input pose: \nprotocols.simple_filters.BuriedUnsatHbondFilter: all_heavy_atom_unsats = 18\nprotocols.simple_filters.BuriedUnsatHbondFilter: bb_heavy_atom_unsats = 12\nprotocols.simple_filters.BuriedUnsatHbondFilter: sc_heavy_atom_unsats = 6\nprotocols.simple_filters.BuriedUnsatHbondFilter: countable_nonheavy_unsats = 14\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 4: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 4: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 32: LEU N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 32: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 32: LEU H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 41: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 41: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 42: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 42: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 58: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 65: ASN 2HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 66: GLN O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 66: GLN NE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 66: GLN 1HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 66: GLN 2HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 101: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 109: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 109: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 110: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 110: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 127: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 128: GLN 2HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 134: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 134: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 172: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 180: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 180: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 181: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 181: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 198: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 205: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 205: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: USER HAS SPECIFIED CUSTOM REPORTING BEHAVIOR FOR # UNSATS\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.vardist_solaccess: VarSolDistSasaCalculator::recompute\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.simple_filters.BuriedUnsatHbondFilter: buried unsats in input pose: \nprotocols.simple_filters.BuriedUnsatHbondFilter: all_heavy_atom_unsats = 18\nprotocols.simple_filters.BuriedUnsatHbondFilter: bb_heavy_atom_unsats = 12\nprotocols.simple_filters.BuriedUnsatHbondFilter: sc_heavy_atom_unsats = 6\nprotocols.simple_filters.BuriedUnsatHbondFilter: countable_nonheavy_unsats = 14\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 4: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 4: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 32: LEU N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 32: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 32: LEU H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 41: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 41: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 42: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 42: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 58: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 65: ASN 2HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 66: GLN O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 66: GLN NE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 66: GLN 1HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 66: GLN 2HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 101: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 109: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 109: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 110: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 110: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 127: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 128: GLN 2HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 134: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 134: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 172: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 180: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 180: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 181: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 181: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 198: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 205: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 205: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: USER HAS SPECIFIED CUSTOM REPORTING BEHAVIOR FOR # UNSATS\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.vardist_solaccess: VarSolDistSasaCalculator::recompute\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.simple_filters.BuriedUnsatHbondFilter: buried unsats in input pose: \nprotocols.simple_filters.BuriedUnsatHbondFilter: all_heavy_atom_unsats = 16\nprotocols.simple_filters.BuriedUnsatHbondFilter: bb_heavy_atom_unsats = 9\nprotocols.simple_filters.BuriedUnsatHbondFilter: sc_heavy_atom_unsats = 7\nprotocols.simple_filters.BuriedUnsatHbondFilter: countable_nonheavy_unsats = 11\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 4: GLU N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 4: GLU H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 32: ARG N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 32: ARG H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 41: TYR OH \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 42: GLU N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 42: GLU H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 56: GLU OE1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 66: TYR O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 101: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 110: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 110: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 116: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 116: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 127: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 127: ASN ND2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 127: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 127: ASN 2HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 128: GLN 2HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 134: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 172: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 181: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 181: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 198: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 199: GLN 1HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 205: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 205: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: USER HAS SPECIFIED CUSTOM REPORTING BEHAVIOR FOR # UNSATS\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////\nprotocols.simple_filters.BuriedUnsatHbondFilter: \nprotocols.vardist_solaccess: VarSolDistSasaCalculator::recompute\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.vardist_solaccess: VarSolDistSasaCalculator::lookup\nprotocols.simple_filters.BuriedUnsatHbondFilter: buried unsats in input pose: \nprotocols.simple_filters.BuriedUnsatHbondFilter: all_heavy_atom_unsats = 16\nprotocols.simple_filters.BuriedUnsatHbondFilter: bb_heavy_atom_unsats = 9\nprotocols.simple_filters.BuriedUnsatHbondFilter: sc_heavy_atom_unsats = 7\nprotocols.simple_filters.BuriedUnsatHbondFilter: countable_nonheavy_unsats = 11\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 4: GLU N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 4: GLU H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 32: ARG N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 32: ARG H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 41: TYR OH \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 42: GLU N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 42: GLU H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 56: GLU OE1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom\u001b[2K\rA 0\nC 0\nD 0\nE 15\nF 4\nG 0\nH 4\nI 2\nK 4\nL 0\nM 10\nN 0\nP 0\nQ 4\nR 12\nS 3\nT 3\nV 0\nW 1\nY 2\nThe % aromatic residues in chain A is 27.142857142857142%\nThe % leucine in chain A is 0.0%\nThe sasa of minimized_start_pose is 10371.981487899207\nThe sasa of designed_relaxed_pose is 11114.383085079851\nThe net charge of chain A = 0\nThe net charge of chain A = 0.0\nThe number of unsatisfied side-chain heavy atoms in minimized_start_pose is 6.0\nThe number of unsatisfied backbone heavy atoms in minimized_start_pose is 12.0\nThe number of unsatisfied side-chain heavy atoms in designed_relaxed_pose is 7.0\nThe number of unsatisfied backbone heavy atoms in designed_relaxed_pose is 9.0\n at residue 66: TYR O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 101: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 110: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 110: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 116: VAL N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 116: VAL H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 127: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 127: ASN ND2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 127: ASN 1HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 127: ASN 2HD2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 128: GLN 2HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 134: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 172: LEU O \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 181: ILE N \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 181: ILE H \nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 198: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 199: GLN 1HE2\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied HEAVY polar atom at residue 205: ASN OD1\nprotocols.simple_filters.BuriedUnsatHbondFilter: Unsatisfied Hpol polar atom at residue 205: ASN 1HD2\n[NbConvertApp] Converting notebook 06.07-Introduction-to-DeNovo-protein-design.ipynb to python\n[NbConvertApp] Writing 36620 bytes to 06.07-Introduction-to-DeNovo-protein-design.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "06.08-Point-Mutation-Scan": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 06.08-Point-Mutation-Scan.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 06.08-Point-Mutation-Scan.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=163242657 seed_offset=0 real_seed=163242657\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=163242657 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1158184360 seed_offset=0 real_seed=-1158184360\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1158184360 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.78856 seconds.\ncore.import_pose.import_pose: File 'inputs/1jhl.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 130 204\ncore.conformation.Conformation: current variant for 130 CYS\ncore.conformation.Conformation: current variant for 204 CYS\ncore.conformation.Conformation: current variant for 130 CYD\ncore.conformation.Conformation: current variant for 204 CYD\ncore.conformation.Conformation: Found disulfide between residues 230 351\ncore.conformation.Conformation: current variant for 230 CYS\ncore.conformation.Conformation: current variant for 351 CYS\ncore.conformation.Conformation: current variant for 230 CYD\ncore.conformation.Conformation: current variant for 351 CYD\ncore.conformation.Conformation: Found disulfide between residues 254 339\ncore.conformation.Conformation: current variant for 254 CYS\ncore.conformation.Conformation: current variant for 339 CYS\ncore.conformation.Conformation: current variant for 254 CYD\ncore.conformation.Conformation: current variant for 339 CYD\ncore.conformation.Conformation: Found disulfide between residues 288 304\ncore.conformation.Conformation: current variant for 288 CYS\ncore.conformation.Conformation: current variant for 304 CYS\ncore.conformation.Conformation: current variant for 288 CYD\ncore.conformation.Conformation: current variant for 304 CYD\ncore.conformation.Conformation: Found disulfide between residues 300 318\ncore.conformation.Conformation: current variant for 300 CYS\ncore.conformation.Conformation: current variant for 318 CYS\ncore.conformation.Conformation: current variant for 300 CYD\ncore.conformation.Conformation: current variant for 318 CYD\nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\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.RelaxScriptManager: Looking for MonomerRelax2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.040\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.051\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.265\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.559\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.581\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.import_pose.import_pose: File 'inputs/1jhl.relax.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: Found disulfide between residues 230 351\ncore.conformation.Conformation: current variant for 230 CYS\ncore.conformation.Conformation: current variant for 351 CYS\ncore.conformation.Conformation: current variant for 230 CYD\ncore.conformation.Conformation: current variant for 351 CYD\ncore.conformation.Conformation: Found disulfide between residues 130 204\ncore.conformation.Conformation: current variant for 130 CYS\ncore.conformation.Conformation: current variant for 204 CYS\ncore.conformation.Conformation: current variant for 130 CYD\ncore.conformation.Conformation: current variant for 204 CYD\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 254 339\ncore.conformation.Conformation: current variant for 254 CYS\ncore.conformation.Conformation: current variant for 339 CYS\ncore.conformation.Conformation: current variant for 254 CYD\ncore.conformation.Conformation: current variant for 339 CYD\ncore.conformation.Conformation: Found disulfide between residues 288 304\ncore.conformation.Conformation: current variant for 288 CYS\ncore.conformation.Conformation: current variant for 304 CYS\ncore.conformation.Conformation: current variant for 288 CYD\ncore.conformation.Conformation: current variant for 304 CYD\ncore.conformation.Conformation: Found disulfide between residues 300 318\ncore.conformation.Conformation: current variant for 3PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPDB file name: inputs/1jhl.clean.pdb\nTotal residues: 353\nSequence: DIELTQSPSYLVASPGETITINCRASKSISKSLAWYQEKPGKTNNLLIYSGSTLQSGIPSRFSGSGSGTDFTLTISSLEPEDFAMYICQQHNEYPWTFGGGTKLEIKRQVQLQQSGAELVRPGASVKLSCKASGYTFISYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCTRDDNYGAMDYWGQGTTVTVKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCHIPCSALLSSDITASVNCAKKIVSDGDGMNAWVAWRKHCKGTDVNVWIRGCRL\nFold tree:\nFOLD_TREE EDGE 1 108 -1 EDGE 1 109 1 EDGE 109 224 -1 EDGE 1 225 2 EDGE 225 353 -1 \n<pyrosetta.rosetta.protocols.relax.FastRelax object at 0x7f43546411f0>\n\nOld Energy: -1056.7706152586127 \n\n\nNew Energy: -1056.7706152586127 \n\n\nBound State Score -1056.7706152586127 \n\n\nUnbound State Score -998.7222019353229 \n\ndG -58.048413323289765 Rosetta Energy Units (REU)\nC\nDIELTQSPSYLVASPGETITINCRASKSISKSLAWYQEKPGKTNNLLIYSGSTLQSGIPSRFSGSGSGTDFTLTISSLEPEDFAMYICQQHNEYPWTFGGGTKLEIKRQVQLQQSGAELVRPGASVKLSCKASGYTFISYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCTRDDNYGAMDYWGQGTTVTVKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCHIPCSALLSSDITASVNCAKKIVSDGDGMNAWVAWRKHCKGTDVNVWIRGCRL\n\n C\nCYS:disulfide (CYS, C):\nBase: CYS\n Properties: POLYMER PROTEIN CANONICAL_AA SC_ORBITALS METALBINDING DISULFIDE_BONDED ALPHA_AA L_AA\n Variant types: DISULFIDE\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB SG 1HB 2HB \n\nCYS\nCYS\nC\n00 CYS\ncore.conformation.Conformation: current variant for 318 CYS\ncore.conformation.Conformation: current variant for 300 CYD\ncore.conformation.Conformation: current variant for 318 CYD\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.339255 seconds to load from binary\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n[NbConvertApp] Converting notebook 06.08-Point-Mutation-Scan.ipynb to python\n[NbConvertApp] Writing 16068 bytes to 06.08-Point-Mutation-Scan.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "07.00-Protein-Docking": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 07.00-Protein-Docking.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 07.00-Protein-Docking.py\n[NbConvertApp] Converting notebook 07.00-Protein-Docking.ipynb to python\n[NbConvertApp] Writing 2938 bytes to 07.00-Protein-Docking.py\n", "state": "passed"}, "07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.py\n[NbConvertApp] Converting notebook 07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb to python\n[NbConvertApp] Writing 2757 bytes to 07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.py\n", "state": "passed"}, "07.02-Docking-Moves-in-Rosetta": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 07.02-Docking-Moves-in-Rosetta.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 07.02-Docking-Moves-in-Rosetta.py\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nWe changed the Jump that was connecting the N-termini of A and B into a Jump that connects the centers of A and B.\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-877960906 seed_offset=0 real_seed=-877960906\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-877960906 RG_type=mt19937\n[NbConvertApp] Converting notebook 07.02-Docking-Moves-in-Rosetta.ipynb to python\n[NbConvertApp] Writing 22858 bytes to 07.02-Docking-Moves-in-Rosetta.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "08.00-Ligand-Docking-PyRosetta": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 08.00-Ligand-Docking-PyRosetta.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 08.00-Ligand-Docking-PyRosetta.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-84756303 seed_offset=0 real_seed=-84756303\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-84756303 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.85301 seconds.\ncore.import_pose.import_pose: File 'inputs/test_lig.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'TPA' from the PDB components dictionary for residue type 'pdb_TPA'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 28 atoms at position 337 in file inputs/test_lig.pdb. Best match rsd_type: pdb_TPA\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C1' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C3' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N on residue pdb_TPA 337\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C10 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C6 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C7 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C8 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C9 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N3 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O10 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O11 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O12 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O13 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O3 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O6 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O7 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O8 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O9 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P3 (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 337 because of missing atom number 4 atom name C1'\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.paPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\rck.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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.338181 seconds to load from binary\ncore.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_TPA\ncore.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 337 pdb_TPA\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1468973205 seed_offset=0 real_seed=-1468973205\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1468973205 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-582741887 seed_offset=0 real_seed=-582741887\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-582741887 RG_type=mt19937\ncore.import_pose.import_pose: File 'expected_outputs/test_lig_0.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 38 atoms at position 337 in file expected_outputs/test_lig_0.pdb. Best match rsd_type: pdb_TPA\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C1' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C3' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N on residue pdb_TPA 337\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C10 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C6 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C7 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C8 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C9 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N3 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O10 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O11 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O12 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O13 (trying to store temperature i\u001b[2K\rPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n<IPython.core.display.HTML object>\n\u001b[2K\r\u001b[2K\rWriting outputs/ligand_refinement_from_command_line.py\nn PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O3 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O6 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O7 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O8 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O9 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P3 (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 337 because of missing atom number 4 atom name C1'\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_TPA\ncore.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 337 pdb_TPA\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n[NbConvertApp] Converting notebook 08.00-Ligand-Docking-PyRosetta.ipynb to python\n[NbConvertApp] Writing 25937 bytes to 08.00-Ligand-Docking-PyRosetta.py\n/bin/sh: 1: pip: not found\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n", "state": "passed"}, "08.01-Ligand-Docking-XMLObjects": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 08.01-Ligand-Docking-XMLObjects.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 08.01-Ligand-Docking-XMLObjects.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1661660144 seed_offset=0 real_seed=1661660144\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1661660144 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.66262 seconds.\ncore.import_pose.import_pose: File 'inputs/test_lig.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'TPA' from the PDB components dictionary for residue type 'pdb_TPA'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 28 atoms at position 337 in file inputs/test_lig.pdb. Best match rsd_type: pdb_TPA\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C1' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C3' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6' on residue pdb_TPA 337\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N on residue pdb_TPA 337\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C10 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C6 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C7 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C8 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom C9 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N3 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom N5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O10 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O11 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O12 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O13 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O3 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O4 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O5 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O6 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O7 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O8 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom O9 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P1 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P2 (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 337 atom P3 (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 337 because of missing atom number 4 atom name C1'\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.26257 seconds to load from binary\ncore.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_TPA\ncore.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 337 pdb_TPA\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<SCOREFXNS>\n\t\t<ScoreFunction name=\"fa_standard\" weights=\"ref2015.wts\"/>\n\t</SCOREFXNS>\n\t<RESIDUE_SELECTORS>\n\t\t<Chain chains=\"X\" name=\"chX\"/>\n\t</RESIDUE_SELECTORS>\n\t<SIMPLE_METRICS>\n\t\t<RMSDMetric name=\"rmsd_chX\" reference_name=\"store_native\" residue_selector=\"chX\" residue_selector_ref=\"chX\" rmsd_type=\"rmsd_all\" robust=\"true\"/>\n\t</SIMPLE_METRICS>\n\t<SCORINGGRIDS ligand_chain=\"X\" width=\"25\">\n\t\t<ClassicGrid grid_name=\"vdw\" weight=\"1.0\"/>\n\t</SCORINGGRIDS>\n\t<LIGAND_AREAS>\n\t\t<LigandArea add_nbr_radius=\"true\" all_atom_mode=\"true\" chain=\"X\" cutoff=\"6.0\" minimize_ligand=\"10\" name=\"docking_sidechain_X\"/>\n\t\t<LigandArea add_nbr_radius=\"true\" all_atom_mode=\"true\" chain=\"X\" cutoff=\"6.0\" name=\"final_sidechain_X\"/>\n\t\t<LigandArea Calpha_restraints=\"0.3\" add_nbr_radius=\"false\" all_atom_mode=\"true\" chain=\"X\" cutoff=\"7.0\" name=\"final_backbone_X\"/>\n\t</LIGAND_AREAS>\n\t<INTERFACE_BUILDERS>\n\t\t<InterfaceBuilder ligand_areas=\"docking_sidechain_X\" name=\"side_chain_for_docking\"/>\n\t\t<InterfaceBuilder ligand_areas=\"final_sidechain_X\" name=\"side_chain_for_final\"/>\n\t\t<InterfaceBuilder extension_window=\"3\" ligand_areas=\"final_backbone_X\" name=\"backbone\"/>\n\t</INTERFACE_BUILDERS>\n\t<MOVEMAP_BUILDERS>\n\t\t<MoveMapBuilder minimize_water=\"true\" name=\"docking\" sc_interface=\"side_chain_for_docking\"/>\n\t\t<MoveMapBuilder bb_interface=\"backbone\" minimize_water=\"true\" name=\"final\" sc_interface=\"side_chain_for_final\"/>\n\t</MOVEMAP_BUILDERS>\n\t<MOVERS>\n\t\t<SavePoseMover name=\"spm\" reference_name=\"store_native\" restore_pose=\"0\"/>\n\t\t<Transform angle=\"360\" box_size=\"20.0\" chain=\"X\" cycles=\"500\" initial_perturb=\"2\" move_distance=\"10\" name=\"transform\" repeats=\"5\" temperature=\"1000\"/>\n\t\t<HighResDocker cycles=\"9\" movemap_builder=\"docking\" name=\"high_res_docker\" repack_every_Nth=\"3\" scorefxn=\"fa_standard\"/>\n\t\t<FinalMinimizer movemap_builder=\"final\" name=\"final\" scorefxn=\"fa_standard\"/>\n\t</MOVERS>\n\t<FILTERS>\n\t\t<LigInterfaceEnergy confidence=\"0\" energy_cutoff=\"0.0\" name=\"interfE\" scorefxn=\"fa_standard\"/>\n\t\t<SimpleMetricFilter comparison_type=\"lt\" confidence=\"0\" cutoff=\"999999.\" metric=\"rmsd_chX\" name=\"rmsd_chX\"/>\n\t</FILTERS>\n\t<PROTOCOLS>\n\t\t<Add mover=\"spm\"/>\n\t\t<Add mover=\"transform\"/>\n\t\t<Add mover=\"high_res_docker\"/>\n\t\t<Add mover=\"final\"/>\n\t\t<Add filter=\"interfE\"/>\n\t\t<Add filter=\"rmsd_chX\"/>\n\t</PROTOCOLS>\n</ROSETTASCRIPTS>\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/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\nprotocols.jd2.parser.ScoreFunctionLoader: defined score function \"fa_standard\" with weights \"ref2015.wts\"\ncore.pose.ref_pose: Loading PDB: store_native\ncore.simple_metrics.metrics.RMSDMetric: Loaded reference pose: store_native with 0 residues\ncore.pose.ref_pose: Loading PDB: store_native\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"spm\" of type SavePoseMover\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"transform\" of type Transform\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"high_res_docker\" of type HighResDocker\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"final\" of type FinalMinimizer\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined filter named \"interfE\" of type LigInterfaceEnergy\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined filter named \"rmsd_chX\" of type SimpleMetricFilter\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"spm\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"transform\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"high_res_docker\"\nprotocols.rosetta_scripts.ParsedProtocol: Added mover \"final\"\nprotocols.rosetta_scripts.ParsedProtocol: Added filter \"interfE\"\nprotocols.rosetta_scripts.ParsedProtocol: Added filter \"rmsd_chX\"\n<IPython.core.display.HTML object>\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1107112851 seed_offset=0 real_seed=1107112851\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1107112851 RG_type=mt19937\n[NbConvertApp] Converting notebook 08.01-Ligand-Docking-XMLObjects.ipynb to python\n[NbConvertApp] Writing 11264 bytes to 08.01-Ligand-Docking-XMLObjects.py\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n", "state": "passed"}, "08.02-Ligand-Docking-pyrosetta.distributed": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 08.02-Ligand-Docking-pyrosetta.distributed.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 08.02-Ligand-Docking-pyrosetta.distributed.py\n<IPython.core.display.HTML object>\n[NbConvertApp] Converting notebook 08.02-Ligand-Docking-pyrosetta.distributed.ipynb to python\n[NbConvertApp] Writing 6228 bytes to 08.02-Ligand-Docking-pyrosetta.distributed.py\nINFO:matplotlib.font_manager:generated new fontManager\n/bin/sh: 1: pip: not found\nINFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'options': '-ignore_unrecognized_res 1 -extra_res_fa inputs/TPA.am1-bcc.gp.params -beta_cart -out:level 200', 'extra_options': '-out:levels all:warning', 'set_logging_handler': 'logging', 'silent': True}\nINFO:pyrosetta.rosetta:Found rosetta database at: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database; using it....\nINFO:pyrosetta.rosetta:PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nINFO:rosetta:core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but either -weights are also specified or this is being used with the genpot score function. Not changing input weights file!\nINFO:rosetta:core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] TPA337 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\nINFO:rosetta:core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] TPA337 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\n", "state": "passed"}, "10.00-Working-With-Symmetry": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 10.00-Working-With-Symmetry.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 10.00-Working-With-Symmetry.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2057016534 seed_offset=0 real_seed=-2057016534\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2057016534 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ignore_unrecognized_res -load_PDB_components false -ignore_zero_occupancy false @inputs/glycan_flags -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-27351702 seed_offset=0 real_seed=-27351702\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-27351702 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 2.72877 seconds.\ncore.import_pose.import_pose: File 'inputs/1jnd.pdb' automatically determined to be of type PDB\ncore.io.util: Found 4 glycan linkages in the structure based on atomic distances\ncore.io.util: Automatic glycan connection is activated.\ncore.io.util: Start reordering residues.\ncore.io.util: Corrected glycan residue order (internal numbering): [401, 402, 403, 404]\ncore.io.util: \ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 404\ncore.io.util: Found 4 glycan linkages in the structure based on atomic distances\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc401 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc402 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man403 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man404 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 401. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 401 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 401. Returning BOGUS ID instead.\ncore.conformation.Conformation: Found disulfide between residues 5 32\ncore.conformation.Conformation: current variant for 5 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 5 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 302 385\ncore.conformation.Conformation: current variant for 302 CYS\ncore.conformation.Conformation: current variant for 385 CYS\ncore.conformation.Conformation: current variant for 302 CYD\ncore.conformation.Conformation: current variant for 385 CYD\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.conformation.symmetry.SymmData: [ WARNING ] Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)\ncore.conformation.symmetry.SymmData: [ WARNING ] Setting jump_group JUMPGROUP1: [master 1] 6:0 7:0 2:0 3:0 4:0 5:0 8:0 9:0 \ncore.conformation.symmetry.SymmData: [ WARNING ] Setting weight of master jump ( jump-id=10 ) to 1.0 (was undefined)\ncore.conformation.symmetry.SymmData: [ WARNING ] Setting jump_group JUMPGROUP2: [master 10] 20:0 22:0 12:0 14:0 16:0 18:0 24:0 26:0 \ncore.conformation.symmetry.SymmData: symmetry name: 1jnd_P_32_2_1\ncore.conformation.symmetry.SymmData: number of subunits: 9\ncore.conformation.symmetry.SymmData: number of interfaces: 1\ncore.conformation.symmetry.SymmData: score subunit number: VRT_0_0_0_0\ncore.conformation.symmetry.SymmData: anchor the subunits at residue: 1\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_0_0_0\ncore.conformation.symmetry.SymmData: x: 1 0 0\ncore.conformation.symmetry.SymmData: y: 0 1 0\ncore.conformation.symmetry.SymmData: origin: 73.8756 49.0221 11.025\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_0_0_0_0_base\ncore.conformation.symmetry.SymmData: x: 1 0 0\ncore.conformation.symmetry.SymmData: y: 0 1 0\ncore.conformation.symmetry.SymmData: origin: 72.8756 48.0221 10.025\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_1_1_0_n1\ncore.conformation.symmetry.SymmData: x: -0.5 0.866025 0\ncore.conformation.symmetry.SymmData: y: -0.866025 -0.5 0\ncore.conformation.symmetry.SymmData: origin: 26.9528 39.4671 -18.9707\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_1_1_0_n1_base\ncore.conformation.symmetry.SymmData: x: -0.5 0.866025 0\ncore.conformation.symmetry.SymmData: y: -0.866025 -0.5 0\ncore.conformation.symmetry.SymmData: origin: 28.3188 39.1011 -19.9707\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_2_1_1_0\ncore.conformation.symmetry.SymmData: x: -0.5 -0.866025 0\ncore.conformation.symmetry.SymmData: y: 0.866025 -0.5 0\ncore.conformation.symmetry.SymmData: origin: 58.6891 3.60826 41.0206\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_2_1_1_0_base\ncore.conformation.symmetry.SymmData: x: -0.5 -0.866025 0\ncore.conformation.symmetry.SymmData: y: 0.866025 -0.5 0\ncore.conformation.symmetry.SymmData: origin: 58.3231 4.97428 40.0206\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_0_n1_0\ncore.conformation.symmetry.SymmData: x: -0.5 0.866025 0\ncore.conformation.symmetry.SymmData: y: 0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 58.6891 -3.60826 -11.025\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_0_n1_0_base\ncore.conformation.symmetry.SymmData: x: -0.5 0.866025 0\ncore.conformation.symmetry.SymmData: y: 0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 58.3231 -4.97428 -10.025\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_1_0_0\ncore.conformation.symmetry.SymmData: x: -0.5 0.866025 0\ncore.conformation.symmetry.SymmData: y: 0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 111.862 88.4892 -11.025\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_3_1_0_0_base\ncore.conformation.symmetry.SymmData: x: -0.5 0.866025 0\ncore.conformation.symmetry.SymmData: y: 0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 111.496 87.1232 -10.025\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_4_2_1_0\ncore.conformation.symmetry.SymmData: x: -0.5 -0.866025 0\ncore.conformation.symmetry.SymmData: y: -0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 80.1253 52.6304 48.9664\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_4_2_1_0_base\ncore.conformation.symmetry.SymmData: x: -0.5 -0.866025 0\ncore.conformation.symmetry.SymmData: y: -0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 81.4913 52.9964 49.9664\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_4_2_1_n1\ncore.conformation.symmetry.SymmData: x: -0.5 -0.866025 0\ncore.conformation.symmetry.SymmData: y: -0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 80.1253 52.6304 -41.0206\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_4_2_1_n1_base\ncore.conformation.symmetry.SymmData: x: -0.5 -0.866025 0\ncore.conformation.symmetry.SymmData: y: -0.866025 0.5 0\ncore.conformation.symmetry.SymmData: origin: 81.4913 52.9964 -40.0206\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_5_0_1_0\ncore.conformation.symmetry.SymmData: x: 1 0 0\ncore.conformation.symmetry.SymmData: y: -0 -1 0\ncore.conformation.symmetry.SymmData: origin: 20.7031 43.0754 18.9707\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_5_0_1_0_base\ncore.conformation.symmetry.SymmData: x: 1 0 0\ncore.conformation.symmetry.SymmData: y: -0 -1 0\ncore.conformation.symmetry.SymmData: origin: 19.7031 44.0754 19.9707\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_5_1_1_0\ncore.conformation.symmetry.SymmData: x: 1 0 0\ncore.conformation.symmetry.SymmData: y: -0 -1 0\ncore.conformation.symmetry.SymmData: origin: 127.048 43.0754 18.9707\ncore.conformation.symmetry.SymmData: Virtual coordinate system VRT_5_1_1_0_base\ncore.conformation.symmetry.SymmData: x: 1 0 0\ncore.conformation.symmetry.SymmData: y: -0 -1 0\ncore.conformation.symmetry.SymmData: origin: 126.048 44.0754 19.9707\ncore.conformation.symmetry.SymmData: Dof for jump: 1\ncore.conformation.symmetry.SymmData: x 0:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: y 0:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: z 0:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: x_angle 1:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: y_angle 1:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: z_angle 1:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: Dof for jump: 10\ncore.conformation.symmetry.SymmData: x 1:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: y 1:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: z 1:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: x_angle 0:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: y_angle 0:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: z_angle 0:0,0:0,0 n2c\ncore.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_com VRT_0_0_0_0 VRT_0_0_0_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_subunit VRT_0_0_0_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_1_1_0_n1 VRT_0_0_0_0 VRT_1_1_0_n1\ncore.conformation.symmetry.SymmData: Jump JUMP_1_1_0_n1_to_com VRT_1_1_0_n1 VRT_1_1_0_n1_base\ncore.conformation.symmetry.SymmData: Jump JUMP_1_1_0_n1_to_subunit VRT_1_1_0_n1_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_2_1_1_0 VRT_0_0_0_0 VRT_2_1_1_0\ncore.conformation.symmetry.SymmData: Jump JUMP_2_1_1_0_to_com VRT_2_1_1_0 VRT_2_1_1_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_2_1_1_0_to_subunit VRT_2_1_1_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_0 VRT_0_0_0_0 VRT_3_0_n1_0\ncore.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_0_to_com VRT_3_0_n1_0 VRT_3_0_n1_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_0_to_subunit VRT_3_0_n1_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_3_1_0_0 VRT_0_0_0_0 VRT_3_1_0_0\ncore.conformation.symmetry.SymmData: Jump JUMP_3_1_0_0_to_com VRT_3_1_0_0 VRT_3_1_0_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_3_1_0_0_to_subunit VRT_3_1_0_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_4_2_1_0 VRT_0_0_0_0 VRT_4_2_1_0\ncore.conformation.symmetry.SymmData: Jump JUMP_4_2_1_0_to_com VRT_4_2_1_0 VRT_4_2_1_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_4_2_1_0_to_subunit VRT_4_2_1_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_4_2_1_n1 VRT_0_0_0_0 VRT_4_2_1_n1\ncore.conformation.symmetry.SymmData: Jump JUMP_4_2_1_n1_to_com VRT_4_2_1_n1 VRT_4_2_1_n1_base\ncore.conformation.symmetry.SymmData: Jump JUMP_4_2_1_n1_to_subunit VRT_4_2_1_n1_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_5_0_1_0 VRT_0_0_0_0 VRT_5_0_1_0\ncore.conformation.symmetry.SymmData: Jump JUMP_5_0_1_0_to_com VRT_5_0_1_0 VRT_5_0_1_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_5_0_1_0_to_subunit VRT_5_0_1_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Jump JUMP_5_1_1_0 VRT_0_0_0_0 VRT_5_1_1_0\ncore.conformation.symmetry.SymmData: Jump JUMP_5_1_1_0_to_com VRT_5_1_1_0 VRT_5_1_1_0_base\ncore.conformation.symmetry.SymmData: Jump JUMP_5_1_1_0_to_subunit VRT_5_1_1_0_base SUBUNIT\ncore.conformation.symmetry.SymmData: Include subunit:\ncore.conformation.symmetry.SymmData: Output subunit:\ncore.conformation.symmetry.SymmData: SlideType: RANDOM\ncore.conformation.symmetry.SymmData: SlideCriteriaType: CEN_DOCK_SCORE\ncore.conformation.symmetry.SymmData: SlideCriteriaVal: AUTOMATIC\ncore.conformation.symmetry.SymmData: SlideOrder: none\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 2 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 3 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 4 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 5 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 6 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 7 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 8 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 9 glycan trees.\ncore.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================\nVRT_0_0_0_0(3637)\n|----#j10#--->VRT_0_0_0_0_base(3638)----#j1#------>1:Sub1A(1-400)\n|----=j11=--->VRT_1_1_0_n1(3643)---j12=10--->VRT_1_1_0_n1_base(3644)----j2=1---->1213:Sub4A(1213-1612)\n|----=j13=--->VRT_2_1_1_0(3645)---j14=10--->VRT_2_1_1_0_base(3646)----j3=1---->1617:Sub5A(1617-2016)\n|----=j15=--->VRT_3_0_n1_0(3647)---j16=10--->VRT_3_0_n1_0_base(3648)----j4=1---->2021:Sub6A(2021-2420)\n|----=j17=--->VRT_3_1_0_0(3649)---j18=10--->VRT_3_1_0_0_base(3650)----j5=1---->2425:Sub7A(2425-2824)\n|----=j19=--->VRT_4_2_1_0(3639)---j20=10--->VRT_4_2_1_0_base(3640)----j6=1---->405:Sub2A(405-804)\n|----=j21=--->VRT_4_2_1_n1(3641)---j22=10--->VRT_4_2_1_n1_base(3642)----j7=1---->809:Sub3A(809-1208)\n|----=j23=--->VRT_5_0_1_0(3651)---j24=10--->VRT_5_0_1_0_base(3652)----j8=1---->2829:Sub8A(2829-3228)\n\\----=j25=--->VRT_5_1_1_0(3653)---j26=10--->VRT_5_1_1_0_base(3654)----j9=1---->3233:Sub9A(3233-3632)\ncore.conformation.symmetry.Conformation: Found disulfide between residues 5 32\ncore.conformation.symmetry.Conformation: current variant for 5 CYD\ncore.conformation.symmetry.Conformation: current variant for 32 CYD\ncore.conformation.symmetry.Conformation: current variant for 5 CYD\ncore.conformation.symmetry.Conformation: current variant for 32 CYD\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 409 to 436\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 813 to 840\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1217 to 1244\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1621 to 1648\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2025 to 2052\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2429 to 2456\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2833 to 2860\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 3237 to 3264\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 5 to 32\ncore.conformation.symmetry.Conformation: Found disulfide between residues 302 385\ncore.conformation.symmetry.Conformation: current variant for 302 CYD\ncore.conformation.symmetry.Conformation: current variant for 385 CYD\ncore.conformation.symmetry.Conformation: current variant for 302 CYD\ncore.conformation.symmetry.Conformation: current variant for 385 CYD\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 706 to 789\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1110 to 1193\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1514 to 1597\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1918 to 2001\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2322 to 2405\ncore.conformation.symmetry.Conformation: Add symPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ncd inputs && make_symmdef_file.pl -r 12 -m CRYST -p inputs/1jnd.pdb.pdb > inputs/1jnd.pdb_crys.symm && cd -\n3654\n<class 'pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation'>\nAssymUnit? equivalent_res\n1 True 0\n2 True 0\n3 True 0\n4 True 0\n5 True 0\n6 True 0\n7 True 0\n8 True 0\n9 True 0\n10 True 0\n11 True 0\n12 True 0\n13 True 0\n14 True 0\n15 True 0\n16 True 0\n17 True 0\n18 True 0\n19 True 0\n20 True 0\n21 True 0\n22 True 0\n23 True 0\n24 True 0\n25 True 0\n26 True 0\n27 True 0\n28 True 0\n29 True 0\n30 True 0\n31 True 0\n32 True 0\n33 True 0\n34 True 0\n35 True 0\n36 True 0\n37 True 0\n38 True 0\n39 True 0\n40 True 0\n41 True 0\n42 True 0\n43 True 0\n44 True 0\n45 True 0\n46 True 0\n47 True 0\n48 True 0\n49 True 0\n50 True 0\n51 True 0\n52 True 0\n53 True 0\n54 True 0\n55 True 0\n56 True 0\n57 True 0\n58 True 0\n59 True 0\n60 True 0\n61 True 0\n62 True 0\n63 True 0\n64 True 0\n65 True 0\n66 True 0\n67 True 0\n68 True 0\n69 True 0\n70 True 0\n71 True 0\n72 True 0\n73 True 0\n74 True 0\n75 True 0\n76 True 0\n77 True 0\n78 True 0\n79 True 0\n80 True 0\n81 True 0\n82 True 0\n83 True 0\n84 True 0\n85 True 0\n86 True 0\n87 True 0\n88 True 0\n89 True 0\n90 True 0\n91 True 0\n92 True 0\n93 True 0\n94 True 0\n95 True 0\n96 True 0\n97 True 0\n98 True 0\n99 True 0\n100 True 0\n101 True 0\n102 True 0\n103 True 0\n104 True 0\n105 True 0\n106 True 0\n107 True 0\n108 True 0\n109 True 0\n110 True 0\n111 True 0\n112 True 0\n113 True 0\n114 True 0\n115 True 0\n116 True 0\n117 True 0\n118 True 0\n119 True 0\n120 True 0\n121 True 0\n122 True 0\n123 True 0\n124 True 0\n125 True 0\n126 True 0\n127 True 0\n128 True 0\n129 True 0\n130 True 0\n131 True 0\n132 True 0\n133 True 0\n134 True 0\n135 True 0\n136 True 0\n137 True 0\n138 True 0\n139 True 0\n140 True 0\n141 True 0\n142 True 0\n143 True 0\n144 True 0\n145 True 0\n146 True 0\n147 True 0\n148 True 0\n149 True 0\n150 True 0\n151 True 0\n152 True 0\n153 True 0\n154 True 0\n155 True 0\n156 True 0\n157 True 0\n158 True 0\n159 True 0\n160 True 0\n161 True 0\n162 True 0\n163 True 0\n164 True 0\n165 True 0\n166 True 0\n167 True 0\n168 True 0\n169 True 0\n170 True 0\n171 True 0\n172 True 0\n173 True 0\n174 True 0\n175 True 0\n176 True 0\n177 True 0\n178 True 0\n179 True 0\n180 True 0\n181 True 0\n182 True 0\n183 True 0\n184 True 0\n185 True 0\n186 True 0\n187 True 0\n188 True 0\n189 True 0\n190 True 0\n191 True 0\n192 True 0\n193 True 0\n194 True 0\n195 True 0\n196 True 0\n197 True 0\n198 True 0\n199 True 0\n200 True 0\n201 True 0\n202 True 0\n203 True 0\n204 True 0\n205 True 0\n206 True 0\n207 True 0\n208 True 0\n209 True 0\n210 True 0\n211 True 0\n212 True 0\n213 True 0\n214 True 0\n215 True 0\n216 True 0\n217 True 0\n218 True 0\n219 True 0\n220 True 0\n221 True 0\n222 True 0\n223 True 0\n224 True 0\n225 True 0\n226 True 0\n227 True 0\n228 True 0\n229 True 0\n230 True 0\n231 True 0\n232 True 0\n233 True 0\n234 True 0\n235 True 0\n236 True 0\n237 True 0\n238 True 0\n239 True 0\n240 True 0\n241 True 0\n242 True 0\n243 True 0\n244 True 0\n245 True 0\n246 True 0\n247 True 0\n248 True 0\n249 True 0\n250 True 0\n251 True 0\n252 True 0\n253 True 0\n254 True 0\n255 True 0\n256 True 0\n257 True 0\n258 True 0\n259 True 0\n260 True 0\n261 True 0\n262 True 0\n263 True 0\n264 True 0\n265 True 0\n266 True 0\n267 True 0\n268 True 0\n269 True 0\n270 True 0\n271 True 0\n272 True 0\n273 True 0\n274 True 0\n275 True 0\n276 True 0\n277 True 0\n278 True 0\n279 True 0\n280 True 0\n281 True 0\n282 True 0\n283 True 0\n284 True 0\n285 True 0\n286 True 0\n287 True 0\n288 True 0\n289 True 0\n290 True 0\n291 True 0\n292 True 0\n293 True 0\n294 True 0\n295 True 0\n296 True 0\n297 True 0\n298 True 0\n299 True 0\n300 True 0\n301 True 0\n302 True 0\n303 True 0\n304 True 0\n305 True 0\n306 True 0\n307 True 0\n308 True 0\n309 True 0\n310 True 0\n311 True 0\n312 True 0\n313 True 0\n314 True 0\n315 True 0\n316 True 0\n317 True 0\n318 True 0\n319 True 0\n320 True 0\n321 True 0\n322 True 0\n323 True 0\n324 True 0\n325 True 0\n326 True 0\n327 True 0\n328 True 0\n329 True 0\n330 True 0\n331 True 0\n332 True 0\n333 True 0\n334 True 0\n335 True 0\n336 True 0\n337 True 0\n338 True 0\n339 True 0\n340 True 0\n341 True 0\n342 True 0\n343 True 0\n344 True 0\n345 True 0\n346 True 0\n347 True 0\n348 True 0\n349 True 0\n350 True 0\n351 True 0\n352 True 0\n353 True 0\n354 True 0\n355 True 0\n356 True 0\n357 True 0\n358 True 0\n359 True 0\n360 True 0\n361 True 0\n362 True 0\n363 True 0\n364 True 0\n365 True 0\n366 True 0\n367 True 0\n368 True 0\n369 True 0\n370 True 0\n371 True 0\n372 True 0\n373 True 0\n374 True 0\n375 True 0\n376 True 0\n377 True 0\n378 True 0\n379 True 0\n380 True 0\n381 True 0\n382 True 0\n383 True 0\n384 True 0\n385 True 0\n386 True 0\n387 True 0\n388 True 0\n389 True 0\n390 True 0\n391 True 0\n392 True 0\n393 True 0\n394 True 0\n395 True 0\n396 True 0\n397 True 0\n398 True 0\n399 True 0\n400 True 0\n401 True 0\n402 True 0\n403 True 0\n404 True 0\n405 False 1\n406 False 2\n407 False 3\n408 False 4\n409 False 5\n410 False 6\n411 False 7\n412 False 8\n413 False 9\n414 False 10\n415 False 11\n416 False 12\n417 False 13\n418 False 14\n419 False 15\n420 False 16\n421 False 17\n422 False 18\n423 False 19\n424 False 20\n425 False 21\n426 False 22\n427 False 23\n428 False 24\n429 False 25\n430 False 26\n431 False 27\n432 False 28\n433 False 29\n434 False 30\n435 False 31\n436 False 32\n437 False 33\n438 False 34\n439 False 35\n440 False 36\n441 False 37\n442 False 38\n443 False 39\n444 False 40\n445 False 41\n446 False 42\n447 False 43\n448 False 44\n449 False 45\n450 False 46\n451 False 47\n452 False 48\n453 False 49\n454 False 50\n455 False 51\n456 False 52\n457 False 53\n458 False 54\n459 False 55\n460 False 56\n461 False 57\n462 False 58\n463 False 59\n464 False 60\n465 False 61\n466 False 62\n467 False 63\n468 False 64\n469 False 65\n470 False 66\n471 False 67\n472 False 68\n473 False 69\n474 False 70\n475 False 71\n476 False 72\n477 False 73\n478 False 74\n479 False 75\n480 False 76\n481 False 77\n482 False 78\n483 False 79\n484 False 80\n485 False 81\n486 False 82\n487 False 83\n488 False 84\n489 False 85\n490 False 86\n491 False 87\n492 False 88\n493 False 89\n494 False 90\n495 False 91\n496 False 92\n497 False 93\n498 False 94\n499 False 95\n500 False 96\n501 False 97\n502 False 98\n503 False 99\n504 False 100\n505 False 101\n506 False 102\n507 False 103\n508 False 104\n509 False 105\n510 False 106\n511 False 107\n512 False 108\n513 False 109\n514 False 110\n515 False 111\n516 False 112\n517 False 113\n518 False 114\n519 False 115\n520 False 116\n521 False 117\n522 False 118\n523 False 119\n524 False 120\n525 False 121\n526 False 122\n527 False 123\n528 False 124\n529 False 125\n530 False 126\n531 False 127\n532 False 128\n533 False 129\n534 False 130\n535 False 131\n536 False 132\n537 False 133\n538 False 134\n539 False 135\n540 False 136\n541 False 137\n542 False 138\n543 False 139\n544 False 140\n545 False 141\n546 False 142\n547 False 143\n548 False 144\n549 False 145\n550 False 146\n551 False 147\n552 False 148\n553 False 149\n554 False 150\n555 False 151\n556 False 152\n557 False 153\n558 False 154\n559 False 155\n560 False 156\n561 False 157\n562 False 158\n563 False 159\n564 False 160\n565 False 161\n566 False 162\n567 False 163\n568 False 164\n569 False 165\n570 False 166\n571 False 167\n572 False 168\n573 False 169\n574 False 170\n575 False 171\n576 False 172\n577 False 173\n578 False 174\n579 False 175\n580 False 176\n581 False 177\n582 False 178\n583 False 179\n584 False 180\n585 False 181\n586 False 182\n587 False 183\n588 False 184\n589 False 185\n590 False 186\n591 False 187\n592 False 188\n593 False 189\n594 False 190\n595 False 191\n596 False 192\n597 False 193\n598 False 194\n599 False 195\n600 False 196\n601 False 197\n602 False 198\n603 False 199\n604 False 200\n605 False 201\n606 False 202\n607 False 203\n608 False 204\n609 False 205\n610 False 206\n611 False 207\n612 False 208\n613 False 209\n614 False 210\n615 False 211\n616 False 212\n617 False 213\n618 False 214\n619 False 215\n620 False 216\n621 False 217\n622 False 218\n623 False 219\n624 False 220\n625 False 221\n626 False 222\n627 False 223\n628 False 224\n629 False 225\n630 False 226\n631 False 227\n632 False 228\n633 False 229\n634 False 230\n635 False 231\n636 False 232\n637 False 233\n638 False 234\n639 False 235\n640 False 236\n641 False 237\n642 False 238\n643 False 239\n644 False 240\n645 False 241\n646 False 242\n647 False 243\n648 False 244\n649 False 245\n650 False 246\n651 False 247\n652 False 248\n653 False 249\n654 False 250\n655 False 251\n656 False 252\n657 False 253\n658 False 254\n659 False 255\n660 False 256\n661 False 257\n662 False 258\n663 False 259\n664 False 260\n665 False 261\n666 False 262\n667 False 263\n668 False 264\n669 False 265\n670 False 266\n671 False 267\n672 False 268\n673 False 269\n674 False 270\n675 False 271\n676 False 272\n677 False 273\n678 False 274\n679 False 275\n680 False 276\n681 False 277\n682 False 278\n683 False 279\n684 False 280\n685 False 281\n686 False 282\n687 False 283\n688 False 284\n689 False 285\n690 False 286\n691 False 287\n692 False 288\n693 False 289\n694 False 290\n695 False 291\n696 False 292\n697 False 293\n698 False 294\n699 False 295\n700 False 296\n701 False 297\n702 False 298\n703 False 299\n704 False 300\n705 False 301\n706 False 302\n707 False 303\n708 False 304\n709 False 305\n710 False 306\n711 False 307\n712 False 308\n713 False 309\n714 False 310\n715 False 311\n716 False 312\n717 False 313\n718 False 314\n719 False 315\n720 False 316\n721 False 317\n722 False 318\n723 False 319\n724 False 320\n725 False 321\n726 False 322\n727 False 323\n728 False 324\n729 False 325\n730 False 326\n731 False 327\n732 False 328\n733 False 329\n734 False 330\n735 False 331\n736 False 332\n737 False 333\n738 False 334\n739 False 335\n740 False 336\n741 False 337\n742 False 338\n743 False 339\n744 False 340\n745 False 341\n746 False 342\n747 False 343\n748 False 344\n749 False 345\n750 False 346\n751 False 347\n752 False 348\n753 False 349\n754 False 350\n755 False 351\n756 False 352\n757 False 353\n758 False 354\n759 False 355\n760 False 356\n761 False 357\n762 False 358\n763 False 359\n764 False 360\n765 False 361\n766 False 362\n767 False 363\n768 False 364\n769 False 365\n770 False 366\n771 False 367\n772 False 368\n773 False 369\n774 False 370\n775 False 371\n776 False 372\n777 False 373\n778 False 374\n779 False 375\n780 False 376\n781 False 377\n782 False 378\n783 False 379\n784 False 380\n785 False 381\n786 False 382\n787 False 383\n788 False 384\n789 False 385\n790 False 386\n791 False 387\n792 False 388\n793 False 389\n794 False 390\n795 False 391\n796 False 392\n797 False 393\n798 False 394\n799 False 395\n800 False 396\n801 False 397\n802 False 398\n803 False 399\n804 False 400\n805 False 401\n806 False 402\n807 False 403\n808 False 404\n809 False 1\n810 False 2\n811 False 3\n812 False 4\n813 False 5\n814 False 6\n815 False 7\n816 False 8\n817 False 9\n818 False 10\n819 False 11\n820 False 12\n821 False 13\n822 False 14\n823 False 15\n824 False 16\n825 False 17\n826 False 18\n827 False 19\n828 False 20\n829 False 21\n830 False 22\n831 False 23\n832 False 24\n833 False 25\n834 False 26\n835 False 27\n836 False 28\n837 False 29\n838 False 30\n839 False 31\n840 False 32\n841 False 33\n842 False 34\n843 False 35\n844 False 36\n845 False 37\n846 False 38\n847 False 39\n848 False 40\n849 False 41\n850 False 42\n851 False 43\n852 False 44\n853 False 45\n854 False 46\n855 False 47\n856 False 48\n857 False 49\n858 False 50\n859 False 51\n860 False 52\n861 False 53\n862 False 54\n863 False 55\n864 False 56\n865 False 57\n866 False 58\n867 False 59\n868 False 60\n869 False 61\n870 False 62\n871 False 63\n872 False 64\n873 False 65\n874 False 66\n875 False 67\n876 False 68\n877 False 69\n878 False 70\n879 False 71\n880 False 72\n881 False 73\n882 False 74\n883 False 75\n884 False 76\n885 False 77\n886 False 78\n887 False 79\n888 False 80\n889 False 81\n890 False 82\n891 False 83\n892 False 84\n893 False 85\n894 False 86\n895 False 87\n896 False 88\n897 False 89\n898 False 90\n899 False 91\n900 False 92\n901 False 93\n902 False 94\n903 False 95\n904 False 96\n905 False 97\n906 False 98\n907 False 99\n908 False 100\n909 False 101\n910 False 102\n911 False 103\n912 False 104\n913 False 105\n914 False 106\n915 False 107\n916 False 108\n917 False 109\n918 False 110\n919 False 111\n920 False 112\n921 False 113\n922 False 114\n923 False 115\n924 False 116\n925 False 117\n926 False 118\n927 False 119\n928 False 120\n929 False 121\n930 False 122\n931 False 123\n932 False 124\n933 False 125\n934 False 126\n935 False 127\n936 False 128\n937 False 129\n938 False 130\n939 False 131\n940 False 132\n941 False 133\n942 False 134\n943 False 135\n944 False 136\n945 False 137\n946 False 138\n947 False 139\n948 False 140\n949 False 141\n950 False 142\n951 False 143\n952 False 144\n953 False 145\n954 False 146\n955 False 147\n956 False 148\n957 False 149\n958 False 150\n959 False 151\n960 False 152\n961 False 153\n962 False 154\n963 False 155\n964 False 156\n965 False 157\n966 False 158\n967 False 159\n968 False 160\n969 False 161\n970 False 162\n971 False 163\n972 False 164\n973 False 165\n974 False 166\n975 False 167\n976 False 168\n977 False 169\n978 False 170\n979 False 171\n980 False 172\n981 False 173\n982 False 174\n983 False 175\n984 False 176\n985 False 177\n986 False 178\n987 False 179\n988 False 180\n989 False 181\n990 False 182\n991 False 183\n992 False 184\n993 False 185\n994 False 186\n995 False 187\n996 False 188\n997 False 189\n998 False 190\n999 False 191\n1000 False 192\n1001 False 193\n1002 False 194\n1003 False 195\n1004 False 196\n1005 False 197\n1006 False 198\n1007 False 199\n1008 False 200\n1009 False 201\n1010 False 202\n1011 False 203\n1012 False 204\n1013 False 205\n1014 False 206\n1015 False 207\n1016 False 208\n1017 False 209\n1018 False 210\n1019 False 211\n1020 False 212\n1021 False 213\n1022 False 214\n1023 False 215\n1024 False 216\n1025 False 217\n1026 False 218\n1027 False 219\n1028 False 220\n1029 False 221\n1030 False 222\n1031 False 223\n1032 False 224\n1033 False 225\n1034 False 226\n1035 False 227\n1036 False 228\n1037 False 229\n1038 False 230\n1039 False 231\n1040 False 232\n1041 False 233\n1042 False 234\n1043 False 235\n1044 False 236\n1045 False 237\n1046 False 238\n1047 False 239\n1048 False 240\n1049 False 241\n1050 False 242\n1051 False 243\n1052 False 244\n1053 False 245\n1054 False 246\n1055 False 247\n1056 False 248\n1057 False 249\n1058 False 250\n1059 False 251\n1060 False 252\n1061 False 253\n1062 False 254\n1063 False 255\n1064 False 256\n1065 False 257\n1066 False 258\n1067 False 259\n1068 False 260\n1069 False 261\n1070 False 262\n1071 False 263\n1072 False 264\n1073 False 265\n1074 False 266\n1075 False 267\n1076 False 268\n1077 False 269\n1078 False 270\n1079 False 271\n1080 False 272\n1081 False 273\n1082 False 274\n1083 False 275\n1084 False 276\n1085 False 277\n1086 False 278\n1087 False 279\n1088 False 280\n1089 False 281\n1090 False 282\n1091 False 283\n1092 False 284\n1093 False 285\n1094 False 286\n1095 False 287\n1096 False 288\n1097 False 289\n1098 False 290\n1099 False 291\n1100 False 292\n1101 False 293\n1102 False 294\n1103 False 295\n1104 False 296\n1105 False 297\n1106 False 298\n1107 False 299\n1108 False 300\n1109 False 301\n1110 False 302\n1111 False 303\n1112 False 304\n1113 False 305\n1114 False 306\n1115 False 307\n1116 False 308\n1117 False 309\n1118 False 310\n1119 False 311\n1120 False 312\n1121 False 313\n1122 False 314\n1123 False 315\n1124 False 316\n1125 False 317\n1126 False 318\n1127 False 319\n1128 False 320\n1129 False 321\n1130 False 322\n1131 False 323\n1132 False 324\n1133 False 325\n1134 False 326\n1135 False 327\n1136 False 328\n1137 False 329\n1138 False 330\n1139 False 331\n1140 False 332\n1141 False 333\n1142 False 334\n1143 False 335\n1144 False 336\n1145 False 337\n1146 False 338\n1147 False 339\n1148 False 340\n1149 False 341\n1150 False 342\n1151 False 343\n1152 False 344\n1153 False 345\n1154 False 346\n1155 False 347\n1156 False 348\n1157 False 349\n1158 False 350\n1159 False 351\n1160 False 352\n1161 False 353\n1162 False 354\n1163 False 355\n1164 False 356\n1165 False 357\n1166 False 358\n1167 False 359\n1168 False 360\n1169 False 361\n1170 False 362\n1171 False 363\n1172 False 364\n1173 False 365\n1174 False 366\n1175 False 367\n1176 False 368\n1177 False 369\n1178 False 370\n1179 False 371\n1180 False 372\n1181 False 373\n1182 False 374\n1183 False 375\n1184 False 376\n1185 False 377\n1186 False 378\n1187 False 379\n1188 False 380\n1189 False 381\n1190 False 382\n1191 False 383\n1192 False 384\n1193 False 385\n1194 False 386\n1195 False 387\n1196 False 388\n1197 False 389\n1198 False 390\n1199 False 391\n1200 False 392\n1201 False 393\n1202 False 394\n1203 False 395\n1204 False 396\n1205 False 397\n1206 False 398\n1207 False 399\n1208 False 400\n1209 False 401\n1210 False 402\n1211 False 403\n1212 False 404\n1213 False 1\n1214 False 2\n1215 False 3\n1216 False 4\n1217 False 5\n1218 False 6\n1219 False 7\n1220 False 8\n1221 False 9\n1222 False 10\n1223 False 11\n1224 False 12\n1225 False 13\n1226 False 14\n1227 False 15\n1228 False 16\n1229 False 17\n1230 False 18\n1231 False 19\n1232 False 20\n1233 False 21\n1234 False 22\n1235 False 23\n1236 False 24\n1237 False 25\n1238 False 26\n1239 False 27\n1240 False 28\n1241 False 29\n1242 False 30\n1243 False 31\n1244 False 32\n1245 False 33\n1246 False 34\n1247 False 35\n1248 False 36\n1249 False 37\n1250 False 38\n1251 False 39\n1252 False 40\n1253 False 41\n1254 False 42\n1255 False 43\n1256 False 44\n1257 False 45\n1258 False 46\n1259 False 47\n1260 False 48\n1261 False 49\n1262 False 50\n1263 False 51\n1264 False 52\n1265 False 53\n1266 False 54\n1267 False 55\n1268 False 56\n1269 False 57\n1270 False 58\n1271 False 59\n1272 False 60\n1273 False 61\n1274 False 62\n1275 False 63\n1276 False 64\n1277 False 65\n1278 False 66\n1279 False 67\n1280 False 68\n1281 False 69\n1282 False 70\n1283 False 71\n1284 False 72\n1285 False 73\n1286 False 74\n1287 False 75\n1288 False 76\n1289 False 77\n1290 False 78\n1291 False 79\n1292 False 80\n1293 False 81\n1294 False 82\n1295 False 83\n1296 False 84\n1297 False 85\n1298 False 86\n1299 False 87\n1300 False 88\n1301 False 89\n1302 False 90\n1303 False 91\n1304 False 92\n1305 False 93\n1306 False 94\n1307 False 95\n1308 False 96\n1309 False 97\n1310 False 98\n1311 False 99\n1312 False 100\n1313 False 101\n1314 False 102\n1315 False 103\n1316 False 104\n1317 False 105\n1318 False 106\n1319 False 107\n1320 False 108\n1321 False 109\n1322 False 110\n1323 False 111\n1324 False 112\n1325 False 113\n1326 False 114\n1327 False 115\n1328 False 116\n1329 False 117\n1330 False 118\n1331 False 119\n1332 False 120\n1333 False 121\n1334 False 122\n1335 False 123\n1336 False 124\n1337 False 125\n1338 False 126\n1339 False 127\n1340 False 128\n1341 False 129\n1342 False 130\n1343 False 131\n1344 False 132\n1345 False 133\n1346 False 134\n1347 False 135\n1348 False 136\n1349 False 137\n1350 False 138\n1351 False 139\n1352 False 140\n1353 False 141\n1354 False 142\n1355 False 143\n1356 False 144\n1357 False 145\n1358 False 146\n1359 False 147\n1360 False 148\n1361 False 149\n1362 False 150\n1363 False 151\n1364 False 152\n1365 False 153\n1366 False 154\n1367 False 155\n1368 False 156\n1369 False 157\n1370 False 158\n1371 False 159\n1372 False 160\n1373 False 161\n1374 False 162\n1375 False 163\n1376 False 164\n1377 False 165\n1378 False 166\n1379 False 167\n1380 False 168\n1381 False 169\n1382 False 170\n1383 False 171\n1384 False 172\n1385 False 173\n1386 False 174\n1387 False 175\n1388 False 176\n1389 False 177\n1390 False 178\n1391 False 179\n1392 False 180\n1393 False 181\n1394 False 182\n1395 False 183\n1396 False 184\n1397 False 185\n1398 False 186\n1399 False 187\n1400 False 188\n1401 False 189\n1402 False 190\n1403 False 191\n1404 False 192\n1405 False 193\n1406 False 194\n1407 False 195\n1408 False 196\n1409 False 197\n1410 False 198\n1411 False 199\n1412 False 200\n1413 False 201\n1414 False 202\n1415 False 203\n1416 False 204\n1417 False 205\n1418 False 206\n1419 False 207\n1420 False 208\n1421 False 209\n1422 False 210\n1423 False 211\n1424 False 212\n1425 False 213\n1426 False 214\n1427 False 215\n1428 False 216\n1429 False 217\n1430 False 218\n1431 False 219\n1432 False 220\n1433 False 221\n1434 False 222\n1435 False 223\n1436 False 224\n1437 False 225\n1438 False 226\n1439 False 227\n1440 False 228\n1441 False 229\n1442 False 230\n1443 False 231\n1444 False 232\n1445 False 233\n1446 False 234\n1447 False 235\n1448 False 236\n1449 False 237\n1450 False 238\n1451 False 239\n1452 False 240\n1453 False 241\n1454 False 242\n1455 False 243\n1456 False 244\n1457 False 245\n1458 False 246\n1459 False 247\n1460 False 248\n1461 False 249\n1462 False 250\n1463 False 251\n1464 False 252\n1465 False 253\n1466 False 254\n1467 False 255\n1468 False 256\n1469 False 257\n1470 False 258\n1471 False 259\n1472 False 260\n1473 False 261\n1474 False 262\n1475 False 263\n1476 False 264\n1477 False 265\n1478 False 266\n1479 False 267\n1480 False 268\n1481 False 269\n1482 False 270\n1483 False 271\n1484 False 272\n1485 False 273\n1486 False 274\n1487 False 275\n1488 False 276\n1489 False 277\n1490 False 278\n1491 False 279\n1492 False 280\n1493 False 281\n1494 False 282\n1495 False 283\n1496 False 284\n1497 False 285\n1498 False 286\n1499 False 287\n1500 False 288\n1501 False 289\n1502 False 290\n1503 False 291\n1504 False 292\n1505 False 293\n1506 False 294\n1507 False 295\n1508 False 296\n1509 False 297\n1510 False 298\n1511 False 299\n1512 False 300\n1513 False 301\n1514 False 302\n1515 False 303\n1516 False 304\n1517 False 305\n1518 False 306\n1519 False 307\n1520 False 308\n1521 False 309\n1522 False 310\n1523 False 311\n1524 False 312\n1525 False 313\n1526 False 314\n1527 False 315\n1528 False 316\n1529 False 317\n1530 False 318\n1531 False 319\n1532 False 320\n1533 False 321\n1534 False 322\n1535 False 323\n1536 False 324\n1537 False 325\n1538 False 326\n1539 False 327\n1540 False 328\n1541 False 329\n1542 False 330\n1543 False 331\n1544 False 332\n1545 False 333\n1546 False 334\n1547 False 335\n1548 False 336\n1549 False 337\n1550 False 338\n1551 False 339\n1552 False 340\n1553 False 341\n1554 False 342\n1555 False 343\n1556 False 344\n1557 False 345\n1558 False 346\n1559 False 347\n1560 False 348\n1561 False 349\n1562 False 350\n1563 False 351\n1564 False 352\n1565 False 353\n1566 False 354\n1567 False 355\n1568 False 356\n1569 False 357\n1570 False 358\n1571 False 359\n1572 False 360\n1573 False 361\n1574 False 362\n1575 False 363\n1576 False 364\n1577 False 365\n1578 False 366\n1579 False 367\n1580 False 368\n1581 False 369\n1582 False 370\n1583 False 371\n1584 False 372\n1585 False 373\n1586 False 374\n1587 False 375\n1588 False 376\n1589 False 377\n1590 False 378\n1591 False 379\n1592 False 380\n1593 False 381\n1594 False 382\n1595 False 383\n1596 False 384\n1597 False 385\n1598 False 386\n1599 False 387\n1600 False 388\n1601 False 389\n1602 False 390\n1603 False 391\n1604 False 392\n1605 False 393\n1606 False 394\n1607 False 395\n1608 False 396\n1609 False 397\n1610 False 398\n1611 False 399\n1612 False 400\n1613 False 401\n1614 False 402\n1615 False 403\n1616 False 404\n1617 False 1\n1618 False 2\n1619 False 3\n1620 False 4\n1621 False 5\n1622 False 6\n1623 False 7\n1624 False 8\n1625 False 9\n1626 False 10\n1627 False 11\n1628 False 12\n1629 False 13\n1630 False 14\n1631 False 15\n1632 False 16\n1633 False 17\n1634 False 18\n1635 False 19\n1636 False 20\n1637 False 21\n1638 False 22\n1639 False 23\n1640 False 24\n1641 False 25\n1642 False 26\n1643 False 27\n1644 False 28\n1645 False 29\n1646 False 30\n1647 False 31\n1648 False 32\n1649 False 33\n1650 False 34\n1651 False 35\n1652 False 36\n1653 False 37\n1654 False 38\n1655 False 39\n1656 False 40\n1657 False 41\n1658 False 42\n1659 False 43\n1660 False 44\n1661 False 45\n1662 False 46\n1663 False 47\n1664 False 48\n1665 False 49\n1666 False 50\n1667 False 51\n1668 False 52\n1669 False 53\n1670 False 54\n1671 False 55\n1672 False 56\n1673 False 57\n1674 False 58\n1675 False 59\n1676 False 60\n1677 False 61\n1678 False 62\n1679 False 63\n1680 False 64\n1681 False 65\n1682 False 66\n1683 False 67\n1684 False 68\n1685 False 69\n1686 False 70\n1687 False 71\n1688 False 72\n1689 False 73\n1690 False 74\n1691 False 75\n1692 False 76\n1693 False 77\n1694 False 78\n1695 False 79\n1696 False 80\n1697 False 81\n1698 False 82\n1699 False 83\n1700 False 84\n1701 False 85\n1702 False 86\n1703 False 87\n1704 False 88\n1705 False 89\n1706 False 90\n1707 False 91\n1708 False 92\n1709 False 93\n1710 False 94\n1711 False 95\n1712 False 96\n1713 False 97\n1714 False 98\n1715 False 99\n1716 False 100\n1717 False 101\n1718 False 102\n1719 False 103\n1720 False 104\n1721 False 105\n1722 False 106\n1723 False 107\n1724 False 108\n1725 False 109\n1726 False 110\n1727 False 111\n1728 False 112\n1729 False 113\n1730 False 114\n1731 False 115\n1732 False 116\n1733 False 117\n1734 False 118\n1735 False 119\n1736 False 120\n1737 False 121\n1738 False 122\n1739 False 123\n1740 False 124\n1741 False 125\n1742 False 126\n1743 False 127\n1744 False 128\n1745 False 129\n1746 False 130\n1747 False 131\n1748 False 132\n1749 False 133\n1750 False 134\n1751 False 135\n1752 False 136\n1753 False 137\n1754 False 138\n1755 False 139\n1756 False 140\n1757 False 141\n1758 False 142\n1759 False 143\n1760 False 144\n1761 False 145\n1762 False 146\n1763 False 147\n1764 False 148\n1765 False 149\n1766 False 150\n1767 False 151\n1768 False 152\n1769 False 153\n1770 False 154\n1771 False 155\n1772 False 156\n1773 False 157\n1774 False 158\n1775 False 159\n1776 False 160\n1777 False 161\n1778 False 162\n1779 False 163\n1780 False 164\n1781 False 165\n1782 False 166\n1783 False 167\n1784 False 168\n1785 False 169\n1786 False 170\n1787 False 171\n1788 False 172\n1789 False 173\n1790 False 174\n1791 False 175\n1792 False 176\n1793 False 177\n1794 False 178\n1795 False 179\n1796 False 180\n1797 False 181\n1798 False 182\n1799 False 183\n1800 False 184\n1801 False 185\n1802 False 186\n1803 False 187\n1804 False 188\n1805 False 189\n1806 False 190\n1807 False 191\n1808 False 192\n1809 False 193\n1810 False 194\n1811 False 195\n1812 False 196\n1813 False 197\n1814 False 198\n1815 False 199\n1816 False 200\n1817 False 201\n1818 False 202\n1819 False 203\n1820 False 204\n1821 False 205\n1822 False 206\n1823 False 207\n1824 False 208\n1825 False 209\n1826 False 210\n1827 False 211\n1828 False 212\n1829 False 213\n1830 False 214\n1831 False 215\n1832 False 216\n1833 False 217\n1834 False 218\n1835 False 219\n1836 False 220\n1837 False 221\n1838 False 222\n1839 False 223\n1840 False 224\n1841 False 225\n1842 False 226\n1843 False 227\n1844 False 228\n1845 False 229\n1846 False 230\n1847 False 231\n1848 False 232\n1849 False 233\n1850 False 234\n1851 False 235\n1852 False 236\n1853 False 237\n1854 False 238\n1855 False 239\n1856 False 240\n1857 False 241\n1858 False 242\n1859 False 243\n1860 False 244\n1861 False 245\n1862 False 246\n1863 False 247\n1864 False 248\n1865 False 249\n1866 False 250\n1867 False 251\n1868 False 252\n1869 False 253\n1870 False 254\n1871 False 255\n1872 False 256\n1873 False 257\n1874 False 258\n1875 False 259\n1876 False 260\n1877 False 261\n1878 False 262\n1879 False 263\n1880 False 264\n1881 False 265\n1882 False 266\n1883 False 267\n1884 False 268\n1885 False 269\n1886 False 270\n1887 False 271\n1888 False 272\n1889 False 273\n1890 False 274\n1891 False 275\n1892 False 276\n1893 False 277\n1894 False 278\n1895 False 279\n1896 False 280\n1897 False 281\n1898 False 282\n1899 False 283\n1900 False 284\n1901 False 285\n1902 False 286\n1903 False 287\n1904 False 288\n1905 False 289\n1906 False 290\n1907 False 291\n1908 False 292\n1909 False 293\n1910 False 294\n1911 False 295\n1912 False 296\n1913 False 297\n1914 False 298\n1915 False 299\n1916 False 300\n1917 False 301\n1918 False 302\n1919 False 303\n1920 False 304\n1921 False 305\n1922 False 306\n1923 False 307\n1924 False 308\n1925 False 309\n1926 False 310\n1927 False 311\n1928 False 312\n1929 False 313\n1930 False 314\n1931 False 315\n1932 False 316\n1933 False 317\n1934 False 318\n1935 False 319\n1936 False 320\n1937 False 321\n1938 False 322\n1939 False 323\n1940 False 324\n1941 False 325\n1942 False 326\n1943 False 327\n1944 False 328\n1945 False 329\n1946 False 330\n1947 False 331\n1948 False 332\n1949 False 333\n1950 False 334\n1951 False 335\n1952 False 336\n1953 False 337\n1954 False 338\n1955 False 339\n1956 False 340\n1957 False 341\n1958 False 342\n1959 False 343\n1960 False 344\n1961 False 345\n1962 False 346\n1963 False 347\n1964 False 348\n1965 False 349\n1966 False 350\n1967 False 351\n1968 False 352\n1969 False 353\n1970 False 354\n1971 False 355\n1972 False 356\n1973 False 357\n1974 False 358\n1975 False 359\n1976 False 360\n1977 False 361\n1978 False 362\n1979 False 363\n1980 False 364\n1981 False 365\n1982 False 366\n1983 False 367\n1984 False 368\n1985 False 369\n1986 False 370\n1987 False 371\n1988 False 372\n1989 False 373\n1990 False 374\n1991 False 375\n1992 False 376\n1993 False 377\n1994 False 378\n1995 False 379\n1996 False 380\n1997 False 381\n1998 False 382\n1999 False 383\n2000 False 384\n2001 False 385\n2002 False 386\n2003 False 387\n2004 False 388\n2005 False 389\n2006 False 390\n2007 False 391\n2008 False 392\n2009 False 393\n2010 False 394\n2011 False 395\n2012 False 396\n2013 False 397\n2014 False 398\n2015 False 399\n2016 False 400\n2017 False 401\n2018 False 402\n2019 False 403\n2020 False 404\n2021 False 1\n2022 False 2\n2023 False 3\n2024 False 4\n2025 False 5\n2026 False 6\n2027 False 7\n2028 False 8\n2029 False 9\n2030 False 10\n2031 False 11\n2032 False 12\n2033 False 13\n2034 False 14\n2035 False 15\n2036 False 16\n2037 False 17\n2038 False 18\n2039 False 19\n2040 False 20\n2041 False 21\n2042 False 22\n2043 False 23\n2044 False 24\n2045 False 25\n2046 False 26\n2047 False 27\n2048 False 28\n2049 False 29\n2050 False 30\n2051 False 31\n2052 False 32\n2053 False 33\n2054 False 34\n2055 False 35\n2056 False 36\n2057 False 37\n2058 False 38\n2059 False 39\n2060 False 40\n2061 False 41\n2062 False 42\n2063 False 43\n2064 False 44\n2065 False 45\n2066 False 46\n2067 False 47\n2068 False 48\n2069 False 49\n2070 False 50\n2071 False 51\n2072 False 52\n2073 False 53\n2074 False 54\n2075 False 55\n2076 False 56\n2077 False 57\n2078 False 58\n2079 False 59\n2080 False 60\n2081 False 61\n2082 False 62\n2083 False 63\n2084 False 64\n2085 False 65\n2086 False 66\n2087 False 67\n2088 False 68\n2089 False 69\n2090 False 70\n2091 False 71\n2092 False 72\n2093 False 73\n2094 False 74\n2095 False 75\n2096 False 76\n2097 False 77\n2098 False 78\n2099 False 79\n2100 False 80\n2101 False 81\n2102 False 82\n2103 False 83\n2104 False 84\n2105 False 85\n2106 False 86\n2107 False 87\n2108 False 88\n2109 False 89\n2110 False 90\n2111 False 91\n2112 False 92\n2113 False 93\n2114 False 94\n2115 False 95\n2116 False 96\n2117 False 97\n2118 False 98\n2119 False 99\n2120 False 100\n2121 False 101\n2122 False 102\n2123 False 103\n2124 False 104\n2125 False 105\n2126 False 106\n2127 False 107\n2128 False 108\n2129 False 109\n2130 False 110\n2131 False 111\n2132 False 112\n2133 False 113\n2134 False 114\n2135 False 115\n2136 False 116\n2137 False 117\n2138 False 118\n2139 False 119\n2140 False 120\n2141 False 121\n2142 False 122\n2143 False 123\n2144 False 124\n2145 False 125\n2146 False 126\n2147 False 127\n2148 False 128\n2149 False 129\n2150 False 130\n2151 False 131\n2152 False 132\n2153 False 133\n2154 False 134\n2155 False 135\n2156 False 136\n2157 False 137\n2158 False 138\n2159 False 139\n2160 False 140\n2161 False 141\n2162 False 142\n2163 False 143\n2164 False 144\n2165 False 145\n2166 False 146\n2167 False 147\n2168 False 148\n2169 False 149\n2170 False 150\n2171 False 151\n2172 False 152\n2173 False 153\n2174 False 154\n2175 False 155\n2176 False 156\n2177 False 157\n2178 False 158\n2179 False 159\n2180 False 160\n2181 False 161\n2182 False 162\n2183 False 163\n2184 False 164\n2185 False 165\n2186 False 166\n2187 False 167\n2188 False 168\n2189 False 169\n2190 False 170\n2191 False 171\n2192 False 172\n2193 False 173\n2194 False 174\n2195 False 175\n2196 False 176\n2197 False 177\n2198 False 178\n2199 False 179\n2200 False 180\n2201 False 181\n2202 False 182\n2203 False 183\n2204 False 184\n2205 False 185\n2206 False 186\n2207 False 187\n2208 False 188\n2209 False 189\n2210 False 190\n2211 False 191\n2212 False 192\n2213 False 193\n2214 False 194\n2215 False 195\n2216 False 196\n2217 False 197\n2218 False 198\n2219 False 199\n2220 False 200\n2221 False 201\n2222 False 202\n2223 False 203\n2224 False 204\n2225 False 205\n2226 False 206\n2227 False 207\n2228 False 208\n2229 False 209\n2230 False 210\n2231 False 211\n2232 False 212\n2233 False 213\n2234 False 214\n2235 False 215\n2236 False 216\n2237 False 217\n2238 False 218\n2239 False 219\n2240 False 220\n2241 False 221\n2242 False 222\n2243 False 223\n2244 False 224\n2245 False 225\n2246 False 226\n2247 False 227\n2248 False 228\n2249 False 229\n2250 False 230\n2251 False 231\n2252 False 232\n2253 False 233\n2254 False 234\n2255 False 235\n2256 False 236\n2257 False 237\n2258 False 238\n2259 False 239\n2260 False 240\n2261 False 241\n2262 False 242\n2263 False 243\n2264 False 244\n2265 False 245\n2266 False 246\n2267 False 247\n2268 False 248\n2269 False 249\n2270 False 250\n2271 False 251\n2272 False 252\n2273 False 253\n2274 False 254\n2275 False 255\n2276 False 256\n2277 False 257\n2278 False 258\n2279 False 259\n2280 False 260\n2281 False 261\n2282 False 262\n2283 False 263\n2284 False 264\n2285 False 265\n2286 False 266\n2287 False 267\n2288 False 268\n2289 False 269\n2290 False 270\n2291 False 271\n2292 False 272\n2293 False 273\n2294 False 274\n2295 False 275\n2296 False 276\n2297 False 277\n2298 False 278\n2299 False 279\n2300 False 280\n2301 False 281\n2302 False 282\n2303 False 283\n2304 False 284\n2305 False 285\n2306 False 286\n2307 False 287\n2308 False 288\n2309 False 289\n2310 False 290\n2311 False 291\n2312 False 292\n2313 False 293\n2314 False 294\n2315 False 295\n2316 False 296\n2317 False 297\n2318 False 298\n2319 False 299\n2320 False 300\n2321 False 301\n2322 False 302\n2323 False 303\n2324 False 304\n2325 False 305\n2326 False 306\n2327 False 307\n2328 False 308\n2329 False 309\n2330 False 310\n2331 False 311\n2332 False 312\n2333 False 313\n2334 False 314\n2335 False 315\n2336 False 316\n2337 False 317\n2338 False 318\n2339 False 319\n2340 False 320\n2341 False 321\n2342 False 322\n2343 False 323\n2344 False 324\n2345 False 325\n2346 False 326\n2347 False 327\n2348 False 328\n2349 False 329\n2350 False 330\n2351 False 331\n2352 False 332\n2353 False 333\n2354 False 334\n2355 False 335\n2356 False 336\n2357 False 337\n2358 False 338\n2359 False 339\n2360 False 340\n2361 False 341\n2362 False 342\n2363 False 343\n2364 False 344\n2365 False 345\n2366 False 346\n2367 False 347\n2368 False 348\n2369 False 349\n2370 False 350\n2371 False 351\n2372 False 352\n2373 False 353\n2374 False 354\n2375 False 355\n2376 False 356\n2377 False 357\n2378 False 358\n2379 False 359\n2380 False 360\n2381 False 361\n2382 False 362\n2383 False 363\n2384 False 364\n2385 False 365\n2386 False 366\n2387 False 367\n2388 False 368\n2389 False 369\n2390 False 370\n2391 False 371\n2392 False 372\n2393 False 373\n2394 False 374\n2395 False 375\n2396 False 376\n2397 False 377\n2398 False 378\n2399 False 379\n2400 False 380\n2401 False 381\n2402 False 382\n2403 False 383\n2404 False 384\n2405 False 385\n2406 False 386\n2407 False 387\n2408 False 388\n2409 False 389\n2410 False 390\n2411 False 391\n2412 False 392\n2413 False 393\n2414 False 394\n2415 False 395\n2416 False 396\n2417 False 397\n2418 False 398\n2419 False 399\n2420 False 400\n2421 False 401\n2422 False 402\n2423 False 403\n2424 False 404\n2425 False 1\n2426 False 2\n2427 False 3\n2428 False 4\n2429 False 5\n2430 False 6\n2431 False 7\n2432 False 8\n2433 False 9\n2434 False 10\n2435 False 11\n2436 False 12\n2437 False 13\n2438 False 14\n2439 False 15\n2440 False 16\n2441 False 17\n2442 False 18\n2443 False 19\n2444 False 20\n2445 False 21\n2446 False 22\n2447 False 23\n2448 False 24\n2449 False 25\n2450 False 26\n2451 False 27\n2452 False 28\n2453 False 29\n2454 False 30\n2455 False 31\n2456 False 32\n2457 False 33\n2458 False 34\n2459 False 35\n2460 False 36\n2461 False 37\n2462 False 38\n2463 False 39\n2464 False 40\n2465 False 41\n2466 False 42\n2467 False 43\n2468 False 44\n2469 False 45\n2470 False 46\n2471 False 47\n2472 False 48\n2473 False 49\n2474 False 50\n2475 False 51\n2476 False 52\n2477 False 53\n2478 False 54\n2479 False 55\n2480 False 56\n2481 False 57\n2482 False 58\n2483 False 59\n2484 False 60\n2485 False 61\n2486 False 62\n2487 False 63\n2488 False 64\n2489 False 65\n2490 False 66\n2491 False 67\n2492 False 68\n2493 False 69\n2494 False 70\n2495 False 71\n2496 False 72\n2497 False 73\n2498 False 74\n2499 False 75\n2500 False 76\n2501 False 77\n2502 False 78\n2503 False 79\n2504 False 80\n2505 False 81\n2506 False 82\n2507 False 83\n2508 False 84\n2509 False 85\n2510 False 86\n2511 False 87\n2512 False 88\n2513 False 89\n2514 False 90\n2515 False 91\n2516 False 92\n2517 False 93\n2518 False 94\n2519 False 95\n2520 False 96\n2521 False 97\n2522 False 98\n2523 False 99\n2524 False 100\n2525 False 101\n2526 False 102\n2527 False 103\n2528 False 104\n2529 False 105\n2530 False 106\n2531 False 107\n2532 False 108\n2533 False 109\n2534 False 110\n2535 False 111\n2536 False 112\n2537 False 113\n2538 False 114\n2539 False 115\n2540 False 116\n2541 False 117\n2542 False 118\n2543 False 119\n2544 False 120\n2545 False 121\n2546 False 122\n2547 False 123\n2548 False 124\n2549 False 125\n2550 False 126\n2551 False 127\n2552 False 128\n2553 False 129\n2554 False 130\n2555 False 131\n2556 False 132\n2557 False 133\n2558 False 134\n2559 False 135\n2560 False 136\n2561 False 137\n2562 False 138\n2563 False 139\n2564 False 140\n2565 False 141\n2566 False 142\n2567 False 143\n2568 False 144\n2569 False 145\n2570 False 146\n2571 False 147\n2572 False 148\n2573 False 149\n2574 False 150\n2575 False 151\n2576 False 152\n2577 False 153\n2578 False 154\n2579 False 155\n2580 False 156\n2581 False 157\n2582 False 158\n2583 False 159\n2584 False 160\n2585 False 161\n2586 False 162\n2587 False 163\n2588 False 164\n2589 False 165\n2590 False 166\n2591 False 167\n2592 False 168\n2593 False 169\n2594 False 170\n2595 False 171\n2596 False 172\n2597 False 173\n2598 False 174\n2599 False 175\n2600 False 176\n2601 False 177\n2602 False 178\n2603 False 179\n2604 False 180\n2605 False 181\n2606 False 182\n2607 False 183\n2608 False 184\n2609 False 185\n2610 False 186\n2611 False 187\n2612 False 188\n2613 False 189\n2614 False 190\n2615 False 191\n2616 False 192\n2617 False 193\n2618 False 194\n2619 False 195\n2620 False 196\n2621 False 197\n2622 False 198\n2623 False 199\n2624 False 200\n2625 False 201\n2626 False 202\n2627 False 203\n2628 False 204\n2629 False 205\n2630 False 206\n2631 False 207\n2632 False 208\n2633 False 209\n2634 False 210\n2635 False 211\n2636 False 212\n2637 False 213\n2638 False 214\n2639 False 215\n2640 False 216\n2641 False 217\n2642 False 218\n2643 False 219\n2644 False 220\n2645 False 221\n2646 False 222\n2647 False 223\n2648 False 224\n2649 False 225\n2650 False 226\n2651 False 227\n2652 False 228\n2653 False 229\n2654 False 230\n2655 False 231\n2656 False 232\n2657 False 233\n2658 False 234\n2659 False 235\n2660 False 236\n2661 False 237\n2662 False 238\n2663 False 239\n2664 False 240\n2665 False 241\n2666 False 242\n2667 False 243\n2668 False 244\n2669 False 245\n2670 False 246\n2671 False 247\n2672 False 248\n2673 False 249\n2674 False 250\n2675 False 251\n2676 False 252\n2677 False 253\n2678 False 254\n2679 False 255\n2680 False 256\n2681 False 257\n2682 False 258\n2683 False 259\n2684 False 260\n2685 False 261\n2686 False 262\n2687 False 263\n2688 False 264\n2689 False 265\n2690 False 266\n2691 False 267\n2692 False 268\n2693 False 269\n2694 False 270\n2695 False 271\n2696 False 272\n2697 False 273\n2698 False 274\n2699 False 275\n2700 False 276\n2701 False 277\n2702 False 278\n2703 False 279\n2704 False 280\n2705 False 281\n2706 False 282\n2707 False 283\n2708 False 284\n2709 False 285\n2710 False 286\n2711 False 287\n2712 False 288\n2713 False 289\n2714 False 290\n2715 False 291\n2716 False 292\n2717 False 293\n2718 False 294\n2719 False 295\n2720 False 296\n2721 False 297\n2722 False 298\n2723 False 299\n2724 False 300\n2725 False 301\n2726 False 302\n2727 False 303\n2728 False 304\n2729 False 305\n2730 False 306\n2731 False 307\n2732 False 308\n2733 False 309\n2734 False 310\n2735 False 311\n2736 False 312\n2737 False 313\n2738 False 314\n2739 False 315\n2740 False 316\n2741 False 317\n2742 False 318\n2743 False 319\n2744 False 320\n2745 False 321\n2746 False 322\n2747 False 323\n2748 False 324\n2749 False 325\n2750 False 326\n2751 False 327\n2752 False 328\n2753 False 329\n2754 False 330\n2755 False 331\n2756 False 332\n2757 False 333\n2758 False 334\n2759 False 335\n2760 False 336\n2761 False 337\n2762 False 338\n2763 False 339\n2764 False 340\n2765 False 341\n2766 False 342\n2767 False 343\n2768 False 344\n2769 False 345\n2770 False 346\n2771 False 347\n2772 False 348\n2773 False 349\n2774 False 350\n2775 False 351\n2776 False 352\n2777 False 353\n2778 False 354\n2779 False 355\n2780 False 356\n2781 False 357\n2782 False 358\n2783 False 359\n2784 False 360\n2785 False 361\n2786 False 362\n2787 False 363\n2788 False 364\n2789 False 365\n2790 False 366\n2791 False 367\n2792 False 368\n2793 False 369\n2794 False 370\n2795 False 371\n2796 False 372\n2797 False 373\n2798 False 374\n2799 False 375\n2800 False 376\n2801 False 377\n2802 False 378\n2803 False 379\n2804 False 380\n2805 False 381\n2806 False 382\n2807 False 383\n2808 False 384\n2809 False 385\n2810 False 386\n2811 False 387\n2812 False 388\n2813 False 389\n2814 False 390\n2815 False 391\n2816 False 392\n2817 False 393\n2818 False 394\n2819 False 395\n2820 False 396\n2821 False 397\n2822 False 398\n2823 False 399\n2824 False 400\n2825 False 401\n2826 False 402\n2827 False 403\n2828 False 404\n2829 False 1\n2830 False 2\n2831 False 3\n2832 False 4\n2833 False 5\n2834 False 6\n2835 False 7\n2836 False 8\n2837 False 9\n2838 False 10\n2839 False 11\n2840 False 12\n2841 False 13\n2842 False 14\n2843 False 15\n2844 False 16\n2845 False 17\n2846 False 18\n2847 False 19\n2848 False 20\n2849 False 21\n2850 False 22\n2851 False 23\n2852 False 24\n2853 False 25\n2854 False 26\n2855 False 27\n2856 False 28\n2857 False 29\n2858 False 30\n2859 False 31\n2860 False 32\n2861 False 33\n2862 False 34\n2863 False 35\n2864 False 36\n2865 False 37\n2866 False 38\n2867 False 39\n2868 False 40\n2869 False 41\n2870 False 42\n2871 False 43\n2872 False 44\n2873 False 45\n2874 False 46\n2875 False 47\n2876 False 48\n2877 False 49\n2878 False 50\n2879 False 51\n2880 False 52\n2881 False 53\n2882 False 54\n2883 False 55\n2884 False 56\n2885 False 57\n2886 False 58\n2887 False 59\n2888 False 60\n2889 False 61\n2890 False 62\n2891 False 63\n2892 False 64\n2893 False 65\n2894 False 66\n2895 False 67\n2896 False 68\n2897 False 69\n2898 False 70\n2899 False 71\n2900 False 72\n2901 False 73\n2902 False 74\n2903 False 75\n2904 False 76\n2905 False 77\n2906 False 78\n2907 False 79\n2908 False 80\n2909 False 81\n2910 False 82\n2911 False 83\n2912 False 84\n2913 False 85\n2914 False 86\n2915 False 87\n2916 False 88\n2917 False 89\n2918 False 90\n2919 False 91\n2920 False 92\n2921 False 93\n2922 False 94\n2923 False 95\n2924 False 96\n2925 False 97\n2926 False 98\n2927 False 99\n2928 False 100\n2929 False 101\n2930 False 102\n2931 False 103\n2932 False 104\n2933 False 105\n2934 False 106\n2935 False 107\n2936 False 108\n2937 False 109\n2938 False 110\n2939 False 111\n2940 False 112\n2941 False 113\n2942 False 114\n2943 False 115\n2944 False 116\n2945 False 117\n2946 False 118\n2947 False 119\n2948 False 120\n2949 False 121\n2950 False 122\n2951 False 123\n2952 False 124\n2953 False 125\n2954 False 126\n2955 False 127\n2956 False 128\n2957 False 129\n2958 False 130\n2959 False 131\n2960 False 132\n2961 False 133\n2962 False 134\n2963 False 135\n2964 False 136\n2965 False 137\n2966 False 138\n2967 False 139\n2968 False 140\n2969 False 141\n2970 False 142\n2971 False 143\n2972 False 144\n2973 False 145\n2974 False 146\n2975 False 147\n2976 False 148\n2977 False 149\n2978 False 150\n2979 False 151\n2980 False 152\n2981 False 153\n2982 False 154\n2983 False 155\n2984 False 156\n2985 False 157\n2986 False 158\n2987 False 159\n2988 False 160\n2989 False 161\n2990 False 162\n2991 False 163\n2992 False 164\n2993 False 165\n2994 False 166\n2995 False 167\n2996 False 168\n2997 False 169\n2998 False 170\n2999 False 171\n3000 False 172\n3001 False 173\n3002 False 174\n3003 False 175\n3004 False 176\n3005 False 177\n3006 False 178\n3007 False 179\n3008 False 180\n3009 False 181\n3010 False 182\n3011 False 183\n3012 False 184\n3013 False 185\n3014 False 186\n3015 False 187\n3016 False 188\n3017 False 189\n3018 False 190\n3019 False 191\n3020 False 192\n3021 False 193\n3022 False 194\n3023 False 195\n3024 False 196\n3025 False 197\n3026 False 198\n3027 False 199\n3028 False 200\n3029 False 201\n3030 False 202\n3031 False 203\n3032 False 204\n3033 False 205\n3034 False 206\n3035 False 207\n3036 False 208\n3037 False 209\n3038 False 210\n3039 False 211\n3040 False 212\n3041 False 213\n3042 False 214\n3043 False 215\n3044 False 216\n3045 False 217\n3046 False 218\n3047 False 219\n3048 False 220\n3049 False 221\n3050 False 222\n3051 False 223\n3052 False 224\n3053 False 225\n3054 False 226\n3055 False 227\n3056 False 228\n3057 False 229\n3058 False 230\n3059 False 231\n3060 False 232\n3061 False 233\n3062 False 234\n3063 False 235\n3064 False 236\n3065 False 237\n3066 False 238\n3067 False 239\n3068 False 240\n3069 False 241\n3070 False 242\n3071 False 243\n3072 False 244\n3073 False 245\n3074 False 246\n3075 False 247\n3076 False 248\n3077 False 249\n3078 False 250\n3079 False 251\n3080 False 252\n3081 False 253\n3082 False 254\n3083 False 255\n3084 False 256\n3085 False 257\n3086 False 258\n3087 False 259\n3088 False 260\n3089 False 261\n3090 False 262\n3091 False 263\n3092 False 264\n3093 False 265\n3094 False 266\n3095 False 267\n3096 False 268\n3097 False 269\n3098 False 270\n3099 False 271\n3100 False 272\n3101 False 273\n3102 False 274\n3103 False 275\n3104 False 276\n3105 False 277\n3106 False 278\n3107 False 279\n3108 False 280\n3109 False 281\n3110 False 282\n3111 False 283\n3112 False 284\n3113 False 285\n3114 False 286\n3115 False 287\n3116 False 288\n3117 False 289\n3118 False 290\n3119 False 291\n3120 False 292\n3121 False 293\n3122 False 294\n3123 False 295\n3124 False 296\n3125 False 297\n3126 False 298\n3127 False 299\n3128 False 300\n3129 False 301\n3130 False 302\n3131 False 303\n3132 False 304\n3133 False 305\n3134 False 306\n3135 False 307\n3136 False 308\n3137 False 309\n3138 False 310\n3139 False 311\n3140 False 312\n3141 False 313\n3142 False 314\n3143 False 315\n3144 False 316\n3145 False 317\n3146 False 318\n3147 False 319\n3148 False 320\n3149 False 321\n3150 False 322\n3151 False 323\n3152 False 324\n3153 False 325\n3154 False 326\n3155 False 327\n3156 False 328\n3157 False 329\n3158 False 330\n3159 False 331\n3160 False 332\n3161 False 333\n3162 False 334\n3163 False 335\n3164 False 336\n3165 False 337\n3166 False 338\n3167 False 339\n3168 False 340\n3169 False 341\n3170 False 342\n3171 False 343\n3172 False 344\n3173 False 345\n3174 False 346\n3175 False 347\n3176 False 348\n3177 False 349\n3178 False 350\n3179 False 351\n3180 False 352\n3181 False 353\n3182 False 354\n3183 False 355\n3184 False 356\n3185 False 357\n3186 False 358\n3187 False 359\n3188 False 360\n3189 False 361\n3190 False 362\n3191 False 363\n3192 False 364\n3193 False 365\n3194 False 366\n3195 False 367\n3196 False 368\n3197 False 369\n3198 False 370\n3199 False 371\n3200 False 372\n3201 False 373\n3202 False 374\n3203 False 375\n3204 False 376\n3205 False 377\n3206 False 378\n3207 False 379\n3208 False 380\n3209 False 381\n3210 False 382\n3211 False 383\n3212 False 384\n3213 False 385\n3214 False 386\n3215 False 387\n3216 False 388\n3217 False 389\n3218 False 390\n3219 False 391\n3220 False 392\n3221 False 393\n3222 False 394\n3223 False 395\n3224 False 396\n3225 False 397\n3226 False 398\n3227 False 399\n3228 False 400\n3229 False 401\n3230 False 402\n3231 False 403\n3232 False 404\n3233 False 1\n3234 False 2\n3235 False 3\n3236 False 4\n3237 False 5\n3238 False 6\n3239 False 7\n3240 False 8\n3241 False 9\n3242 False 10\n3243 False 11\n3244 False 12\n3245 False 13\n3246 False 14\n3247 False 15\n3248 False 16\n3249 False 17\n3250 False 18\n3251 False 19\n3252 False 20\n3253 False 21\n3254 False 22\n3255 False 23\n3256 False 24\n3257 False 25\n3258 False 26\n3259 False 27\n3260 False 28\n3261 False 29\n3262 False 30\n3263 False 31\n3264 False 32\n3265 False 33\n3266 False 34\n3267 False 35\n3268 False 36\n3269 False 37\n3270 False 38\n3271 False 39\n3272 False 40\n3273 False 41\n3274 False 42\n3275 False 43\n3276 False 44\n3277 False 45\n3278 False 46\n3279 False 47\n3280 False 48\n3281 False 49\n3282 False 50\n3283 False 51\n3284 False 52\n3285 False 53\n3286 False 54\n3287 False 55\n3288 False 56\n3289 False 57\n3290 False 58\n3291 False 59\n3292 False 60\n3293 False 61\n3294 False 62\n3295 False 63\n3296 False 64\n3297 False 65\n3298 False 66\n3299 False 67\n3300 False 68\n3301 False 69\n3302 False 70\n3303 False 71\n3304 False 72\n3305 False 73\n3306 False 74\n3307 False 75\n3308 False 76\n3309 False 77\n3310 False 78\n3311 False 79\n3312 False 80\n3313 False 81\n3314 False 82\n3315 False 83\n3316 False 84\n3317 False 85\n3318 False 86\n3319 False 87\n3320 False 88\n3321 False 89\n3322 False 90\n3323 False 91\n3324 False 92\n3325 False 93\n3326 False 94\n3327 False 95\n3328 False 96\n3329 False 97\n3330 False 98\n3331 False 99\n3332 False 100\n3333 False 101\n3334 False 102\n3335 False 103\n3336 False 104\n3337 False 105\n3338 False 106\n3339 False 107\n3340 False 108\n3341 False 109\n3342 False 110\n3343 False 111\n3344 False 112\n3345 False 113\n3346 False 114\n3347 False 115\n3348 False 116\n3349 False 117\n3350 False 118\n3351 False 119\n3352 False 120\n3353 False 121\n3354 False 122\n3355 False 123\n3356 False 124\n3357 False 125\n3358 False 126\n3359 False 127\n3360 False 128\n3361 False 129\n3362 False 130\n3363 False 131\n3364 False 132\n3365 False 133\n3366 False 134\n3367 False 135\n3368 False 136\n3369 False 137\n3370 False 138\n3371 False 139\n3372 False 140\n3373 False 141\n3374 False 142\n3375 False 143\n3376 False 144\n3377 False 145\n3378 False 146\n3379 False 147\n3380 False 148\n3381 False 149\n3382 False 150\n3383 False 151\n3384 False 152\n3385 False 153\n3386 False 154\n3387 False 155\n3388 False 156\n3389 False 157\n3390 False 158\n3391 False 159\n3392 False 160\n3393 False 161\n3394 False 162\n3395 False 163\n3396 False 164\n3397 False 165\n3398 False 166\n3399 False 167\n3400 False 168\n3401 False 169\n3402 False 170\n3403 False 171\n3404 False 172\n3405 False 173\n3406 False 174\n3407 False 175\n3408 False 176\n3409 False 177\n3410 False 178\n3411 False 179\n3412 False 180\n3413 False 181\n3414 False 182\n3415 False 183\n3416 False 184\n3417 False 185\n3418 False 186\n3419 False 187\n3420 False 188\n3421 False 189\n3422 False 190\n3423 False 191\n3424 False 192\n3425 False 193\n3426 False 194\n3427 False 195\n3428 False 196\n3429 False 197\n3430 False 198\n3431 False 199\n3432 False 200\n3433 False 201\n3434 False 202\n3435 False 203\n3436 False 204\n3437 False 205metric chemical bond 2726 to 2809\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 3130 to 3213\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 3534 to 3617\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 302 to 385\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 9 glycan trees.\nprotocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...\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: The -include_sugars flag was used with no sugar_bb weight set in the weights file. Setting sugar_bb weight to 0.5 by default.\ncore.scoring.ScoringManager: Creating CHI Energy Function.\ncore.scoring.carbohydrates.CHIEnergyFunction: Setting up chi sampling\ncore.scoring.ScoringManager: Creating carbohydrate omega preferences function.\ncore.scoring.carbohydrates.OmegaPreferencesFunction: Setting up omega preference sampling\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used without fa_intra_rep_xover4 term in the scorefunction. Setting this term's weight to 0.55. It is generally recommended to use the -beta scorefunction (Rosetta-ICO) with sugars, which includes this and other desired terms such as those bridging waters\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.25092 seconds to load from binary\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 2 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 3 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 4 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 5 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 6 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 7 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 8 glycan trees.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 9 glycan trees.\ncore.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================\nVRT_0_0_0_0(3637)\n|----#j10#--->VRT_0_0_0_0_base(3638)----#j1#------>1:Sub1A(1-400)\n|----=j11=--->VRT_1_1_0_n1(3643)---j12=10--->VRT_1_1_0_n1_base(3644)----j2=1---->1213:Sub4A(1213-1612)\n|----=j13=--->VRT_2_1_1_0(3645)---j14=10--->VRT_2_1_1_0_base(3646)----j3=1---->1617:Sub5A(1617-2016)\n|----=j15=--->VRT_3_0_n1_0(3647)---j16=10--->VRT_3_0_n1_0_base(3648)----j4=1---->2021:Sub6A(2021-2420)\n|----=j17=--->VRT_3_1_0_0(3649)---j18=10--->VRT_3_1_0_0_base(3650)----j5=1---->2425:Sub7A(2425-2824)\n|----=j19=--->VRT_4_2_1_0(3639)---j20=10--->VRT_4_2_1_0_base(3640)----j6=1---->405:Sub2A(405-804)\n|----=j21=--->VRT_4_2_1_n1(3641)---j22=10--->VRT_4_2_1_n1_base(3642)----j7=1---->809:Sub3A(809-1208)\n|----=j23=--->VRT_5_0_1_0(3651)---j24=10--->VRT_5_0_1_0_base(3652)----j8=1---->2829:Sub8A(2829-3228)\n\\----=j25=--->VRT_5_1_1_0(3653)---j26=10--->VRT_5_1_1_0_base(3654)----j9=1---->3233:Sub9A(3233-3632)\ncore.conformation.symmetry.Conformation: Found disulfide between residues 5 32\ncore.conformation.symmetry.Conformation: current variant for 5 CYD\ncore.conformation.symmetry.Conformation: current variant for 32 CYD\ncore.conformation.symmetry.Conformation: current variant for 5 CYD\ncore.conformation.symmetry.Conformation: current variant for 32 CYD\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 409 to 436\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 813 to 840\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1217 to 1244\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1621 to 1648\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2025 to 2052\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2429 to 2456\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2833 to 2860\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 3237 to 3264\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 5 to 32\ncore.conformation.symmetry.Conformation: Found disulfide between residues 302 385\ncore.conformation.symmetry.Conformation: current variant for 302 CYD\ncore.conformation.symmetry.Conformation: current variant for 385 CYD\ncore.conformation.symmetry.Conformation: current variant for 302 CYD\ncore.conformation.symmetry.Conformation: current variant for 385 CYD\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 706 to 789\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1110 to 1193\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1514 to 1597\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 1918 to 2001\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 2322 to 2405\ncore.conformation.symmetry.Conformatio\n3438 False 206\n3439 False 207\n3440 False 208\n3441 False 209\n3442 False 210\n3443 False 211\n3444 False 212\n3445 False 213\n3446 False 214\n3447 False 215\n3448 False 216\n3449 False 217\n3450 False 218\n3451 False 219\n3452 False 220\n3453 False 221\n3454 False 222\n3455 False 223\n3456 False 224\n3457 False 225\n3458 False 226\n3459 False 227\n3460 False 228\n3461 False 229\n3462 False 230\n3463 False 231\n3464 False 232\n3465 False 233\n3466 False 234\n3467 False 235\n3468 False 236\n3469 False 237\n3470 False 238\n3471 False 239\n3472 False 240\n3473 False 241\n3474 False 242\n3475 False 243\n3476 False 244\n3477 False 245\n3478 False 246\n3479 False 247\n3480 False 248\n3481 False 249\n3482 False 250\n3483 False 251\n3484 False 252\n3485 False 253\n3486 False 254\n3487 False 255\n3488 False 256\n3489 False 257\n3490 False 258\n3491 False 259\n3492 False 260\n3493 False 261\n3494 False 262\n3495 False 263\n3496 False 264\n3497 False 265\n3498 False 266\n3499 False 267\n3500 False 268\n3501 False 269\n3502 False 270\n3503 False 271\n3504 False 272\n3505 False 273\n3506 False 274\n3507 False 275\n3508 False 276\n3509 False 277\n3510 False 278\n3511 False 279\n3512 False 280\n3513 False 281\n3514 False 282\n3515 False 283\n3516 False 284\n3517 False 285\n3518 False 286\n3519 False 287\n3520 False 288\n3521 False 289\n3522 False 290\n3523 False 291\n3524 False 292\n3525 False 293\n3526 False 294\n3527 False 295\n3528 False 296\n3529 False 297\n3530 False 298\n3531 False 299\n3532 False 300\n3533 False 301\n3534 False 302\n3535 False 303\n3536 False 304\n3537 False 305\n3538 False 306\n3539 False 307\n3540 False 308\n3541 False 309\n3542 False 310\n3543 False 311\n3544 False 312\n3545 False 313\n3546 False 314\n3547 False 315\n3548 False 316\n3549 False 317\n3550 False 318\n3551 False 319\n3552 False 320\n3553 False 321\n3554 False 322\n3555 False 323\n3556 False 324\n3557 False 325\n3558 False 326\n3559 False 327\n3560 False 328\n3561 False 329\n3562 False 330\n3563 False 331\n3564 False 332\n3565 False 333\n3566 False 334\n3567 False 335\n3568 False 336\n3569 False 337\n3570 False 338\n3571 False 339\n3572 False 340\n3573 False 341\n3574 False 342\n3575 False 343\n3576 False 344\n3577 False 345\n3578 False 346\n3579 False 347\n3580 False 348\n3581 False 349\n3582 False 350\n3583 False 351\n3584 False 352\n3585 False 353\n3586 False 354\n3587 False 355\n3588 False 356\n3589 False 357\n3590 False 358\n3591 False 359\n3592 False 360\n3593 False 361\n3594 False 362\n3595 False 363\n3596 False 364\n3597 False 365\n3598 False 366\n3599 False 367\n3600 False 368\n3601 False 369\n3602 False 370\n3603 False 371\n3604 False 372\n3605 False 373\n3606 False 374\n3607 False 375\n3608 False 376\n3609 False 377\n3610 False 378\n3611 False 379\n3612 False 380\n3613 False 381\n3614 False 382\n3615 False 383\n3616 False 384\n3617 False 385\n3618 False 386\n3619 False 387\n3620 False 388\n3621 False 389\n3622 False 390\n3623 False 391\n3624 False 392\n3625 False 393\n3626 False 394\n3627 False 395\n3628 False 396\n3629 False 397\n3630 False 398\n3631 False 399\n3632 False 400\n3633 False 401\n3634 False 402\n3635 False 403\n3636 False 404\n3637 True 0\n3638 True 0\n3639 True 0\n3640 True 0\n3641 True 0\n3642 True 0\n3643 True 0\n3644 True 0\n3645 True 0\n3646 True 0\n3647 True 0\n3648 True 0\n3649 True 0\n3650 True 0\n3651 True 0\n3652 True 0\n3653 True 0\n3654 True 0\nResidue 3654: VRT (XXX, X):\nBase: VRT\n Properties: LIGAND VIRTUAL_RESIDUE\n Variant types:\n Main-chain atoms:\n Backbone atoms: \n Side-chain atoms: ORIG X Y \nAtom Coordinates:\n ORIG: 126.048, 44.0754, 19.9707 (virtual)\n X : 127.048, 44.0754, 19.9707 (virtual)\n Y : 126.048, 43.0754, 19.9707 (virtual)\nMirrored relative to coordinates in ResidueType: FALSE\n\nTotal Subunits: 9.0\nTotal Subunits: 9\n-417.88657273887713\n-905.9936749391034\npacked -932.0454499426537\nn: Add symmetric chemical bond 2726 to 2809\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 3130 to 3213\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 3534 to 3617\ncore.conformation.symmetry.Conformation: Add symmetric chemical bond 302 to 385\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 9 glycan trees.\nprotocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...\n[NbConvertApp] Converting notebook 10.00-Working-With-Symmetry.ipynb to python\n[NbConvertApp] Writing 11571 bytes to 10.00-Working-With-Symmetry.py\n/bin/sh: 1: pip: not found\n10.00-Working-With-Symmetry.py:196: 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.pack.task import *\n", "state": "passed"}, "11.00-Working-With-Density": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 11.00-Working-With-Density.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 11.00-Working-With-Density.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=2001796312 seed_offset=0 real_seed=2001796312\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=2001796312 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ignore_unrecognized_res -load_PDB_components false -ignore_zero_occupancy false @inputs/glycan_flags -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1991715679 seed_offset=0 real_seed=-1991715679\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1991715679 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 2.98812 seconds.\ncore.import_pose.import_pose: File 'inputs/1jnd.pdb' automatically determined to be of type PDB\ncore.io.util: Found 4 glycan linkages in the structure based on atomic distances\ncore.io.util: Automatic glycan connection is activated.\ncore.io.util: Start reordering residues.\ncore.io.util: Corrected glycan residue order (internal numbering): [401, 402, 403, 404]\ncore.io.util: \ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 404\ncore.io.util: Found 4 glycan linkages in the structure based on atomic distances\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc401 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc402 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man403 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man404 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 401. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 401 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 401. Returning BOGUS ID instead.\ncore.conformation.Conformation: Found disulfide between residues 5 32\ncore.conformation.Conformation: current variant for 5 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 5 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 302 385\ncore.conformation.Conformation: current variant for 302 CYS\ncore.conformation.Conformation: current variant for 385 CYS\ncore.conformation.Conformation: current variant for 302 CYD\ncore.conformation.Conformation: current variant for 385 CYD\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<MOVERS>\n\t\t<LoadDensityMap mapfile=\"inputs/1jnd_2mFo-DFc_map.ccp4\" name=\"loaddens\"/>\n\t</MOVERS>\n\t<PROTOCOLS/>\n</ROSETTASCRIPTS>\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: The -include_sugars flag was used with no sugar_bb weight set in the weights file. Setting sugar_bb weight to 0.5 by default.\ncore.scoring.ScoringManager: Creating CHI Energy Function.\ncore.scoring.carbohydrates.CHIEnergyFunction: Setting up chi sampling\ncore.scoring.ScoringManager: Creating carbohydrate omega preferences function.\ncore.scoring.carbohydrates.OmegaPreferencesFunction: Setting up omega preference sampling\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used without fa_intra_rep_xover4 term in the scorefunction. Setting this term's weight to 0.55. It is generally recommended to use the -beta scorefunction (Rosetta-ICO) with sugars, which includes this and other desired terms such as those bridging waters\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\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"loaddens\" of type LoadDensityMap\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\ncore.scoring.electron_density.ElectronDensity: Loading Density Map\ncore.scoring.electron_density.ElectronDensity: Loading density mapinputs/1jnd_2mFo-DFc_map.ccp4\ncore.scoring.electron_density.ElectronDensity: Setting resolution to AUTO\ncore.scoring.electron_density.ElectronDensity: atom mask to 3.2A\ncore.scoring.electron_density.ElectronDensity: CA mask to 6A\ncore.scoring.electron_density.ElectronDensity: Read density map'inputs/1jnd_2mFo-DFc_map.ccp4'\ncore.scoring.electron_density.ElectronDensity: extent: 218 x 229 x 265\ncore.scoring.electron_density.ElectronDensity: origin: -66 x 82 x 209\ncore.scoring.electron_density.ElectronDensity: altorigin: 0 x 0 x 0\ncore.scoring.electron_density.ElectronDensity: grid: 360 x 360 x 288\ncore.scoring.electron_density.ElectronDensity: celldim: 106.345 x 106.345 x 89.987\ncore.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 120\ncore.scoring.electron_density.ElectronDensity: voxel vol.: 0.0236128\ncore.scoring.electron_density.ElectronDensity: Effective resolution = 0.937365\ncore.import_pose.import_pose: File 'inputs/1jnd_refined.pdb.gz' automatically determined to be of type PDB\ncore.io.util: Found 4 glycan linkages in the structure based on atomic distances\ncore.io.util: Automatic glycan connection is activated.\ncore.io.util: Start reordering residues.\ncore.io.util: Corrected glycan residue order (internal numbering): [401, 402, 403, 404]\ncore.io.util: \ncore.io.util: Found 4 glycan linkages in the structure based on atomic distances\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc401 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc402 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man403 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man404 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 401. Returning BOGUS ID instead.\ncore.conformation.Conformation: Found disulfide between residues 5 32\ncore.conformation.Conformation: current variant for 5 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 5 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 302 385\ncore.conformation.Conformation: current variant for 302 CYS\ncore.conformation.Conformation: current variant for 385 CYS\ncore.conformation.Conformation: current variant for 302 CYD\ncore.conformation.Conformation: current variant for 385 CYD\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used with no sugar_bb weight set in the weights file. Setting sugar_bb weight to 0.5 by default.\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used without fa_intra_rep_xover4 term in the scorefunction. Setting this term's weight to 0.55. It is generally recommended to use the -beta scorefunction (Rosetta-ICO) with sugars, which includes this and other desired terms such as those bridging waters\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used with no sugar_bb weight set in the weights file. Setting sugar_bb weight to 0.5 by default.\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used without fa_intra_rep_xover4 term in the scorefunPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\ncrystal -6855.403062869523\nrefined -7689.725496723437\n-6855.403062869523\n-6855.403062869523\nction. Setting this term's weight to 0.55. It is generally recommended to use the -beta scorefunction (Rosetta-ICO) with sugars, which includes this and other desired terms such as those bridging waters\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]\ncore.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=0 / 0 / 0 / 8.60156 sum=(0,0)\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.255826 seconds to load from binary\ncore.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\ncore.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\ncore.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors.\n[NbConvertApp] Converting notebook 11.00-Working-With-Density.ipynb to python\n[NbConvertApp] Writing 9609 bytes to 11.00-Working-With-Density.py\n/bin/sh: 1: pip: not found\n11.00-Working-With-Density.py:119: 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.cryst import *\n", "state": "passed"}, "12.00-Working-With-Antibodies": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 12.00-Working-With-Antibodies.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 12.00-Working-With-Antibodies.py\n[NbConvertApp] Converting notebook 12.00-Working-With-Antibodies.ipynb to python\n[NbConvertApp] Writing 5160 bytes to 12.00-Working-With-Antibodies.py\n", "state": "passed"}, "12.01-RosettaAntibody-Framework-and-SimpleMetrics": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 12.01-RosettaAntibody-Framework-and-SimpleMetrics.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1317237998 seed_offset=0 real_seed=1317237998\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1317237998 RG_type=mt19937\ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -use_input_sc -ignore_unrecognized_res -ignore_zero_occupancy false -load_PDB_components false -no_fconfig -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1056431644 seed_offset=0 real_seed=1056431644\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1056431644 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.82844 seconds.\ncore.import_pose.import_pose: File 'inputs/2r0l_1_1.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 108\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 225\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 464\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: current variant for 23 CYS\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 23 CYD\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: Found disulfide between residues 130 204\ncore.conformation.Conformation: current variant for 130 CYS\ncore.conformation.Conformation: current variant for 204 CYS\ncore.conformation.Conformation: current variant for 130 CYD\ncore.conformation.Conformation: current variant for 204 CYD\ncore.conformation.Conformation: Found disulfide between residues 250 266\ncore.conformation.Conformation: current variant for 250 CYS\ncore.conformation.Conformation: current variant for 266 CYS\ncore.conformation.Conformation: current variant for 250 CYD\ncore.conformation.Conformation: current variant for 266 CYD\ncore.conformation.Conformation: Found disulfide between residues 258 328\ncore.conformation.Conformation: current variant for 258 CYS\ncore.conformation.Conformation: current variant for 328 CYS\ncore.conformation.Conformation: current variant for 258 CYD\ncore.conformation.Conformation: current variant for 328 CYD\ncore.conformation.Conformation: Found disulfide between residues 353 422\ncore.conformation.Conformation: current variant for 353 CYS\ncore.conformation.Conformation: current variant for 422 CYS\ncore.conformation.Conformation: current variant for 353 CYD\ncore.conformation.Conformation: current variant for 422 CYD\ncore.conformation.Conformation: Found disulfide between residues 385 401\ncore.conformation.Conformation: current variant for 385 CYS\ncore.conformation.Conformation: current variant for 401 CYS\ncore.conformation.Conformation: current variant for 385 CYD\ncore.conformation.Conformation: current variant for 401 CYD\ncore.conformation.Conformation: Found disulfide between residues 412 440\ncore.conformation.Conformation: current variant for 412 CYS\ncore.conformation.Conformation: current variant for 440 CYS\ncore.conformation.Conformation: current variant for 412 CYD\ncore.conformation.Conformation: current variant for 440 CYD\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: ARFWWRSFDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR PyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n////////////////////////////////////////////////////////////////////////////////\n/// Rosetta Antibody Info ///\n/// ///\n/// Antibody Type: Regular Antibody\n/// Light Chain Type: unknown\n/// Predict H3 Cterminus Base: KINKED\n/// \n/// H1 info: \n/// length: 13\n/// sequence: AASGFTISNSGIH\n/// north_cluster: H1-13-1\n/// loop_info: LOOP start: 131 stop: 143 cut: 137 size: 13 skip rate: 0 extended?: False\n\n/// H2 info: \n/// length: 10\n/// sequence: WIYPTGGATD\n/// north_cluster: H2-10-1\n/// loop_info: LOOP start: 158 stop: 167 cut: 163 size: 10 skip rate: 0 extended?: False\n\n/// H3 info: \n/// length: 10\n/// sequence: ARFWWRSFDY\n/// north_cluster: H3-10-1\n/// loop_info: LOOP start: 205 stop: 214 cut: 206 size: 10 skip rate: 0 extended?: False\n\n/// L1 info: \n/// length: 11\n/// sequence: RASQDVSTAVA\n/// north_cluster: L1-11-1\n/// loop_info: LOOP start: 24 stop: 34 cut: 29 size: 11 skip rate: 0 extended?: False\n\n/// L2 info: \n/// length: 8\n/// sequence: YSASFLYS\n/// north_cluster: L2-8-1\n/// loop_info: LOOP start: 49 stop: 56 cut: 53 size: 8 skip rate: 0 extended?: False\n\n/// L3 info: \n/// length: 9\n/// sequence: QQSYTTPPT\n/// north_cluster: L3-9-cis7-1\n/// loop_info: LOOP start: 89 stop: 97 cut: 93 size: 9 skip rate: 0 extended?: False\n\n////////////////////////////////////////////////////////////////////////////////\n\nh1 131\nh2 167\n1 H1\n2 H2\n3 H3\n4 L1\n5 L2\n6 L3\nL1 CDRNameEnum.l1\nl1 CDRNameEnum.l1\nL2 CDRNameEnum.l2\nl2 CDRNameEnum.l2\nL3 CDRNameEnum.l3\nH1 CDRNameEnum.h1\nH2 CDRNameEnum.h2\nH3 CDRNameEnum.h3\nCDRNameEnum.h3\n3\nAHO_Scheme\nNorth\nCDRNameEnum.h1\nframework_region\n1 framework_region\n2 framework_region\n3 framework_region\n4 framework_region\n5 framework_region\n6 framework_region\n7 framework_region\n8 framework_region\n9 framework_region\n10 framework_region\n11 framework_region\n12 framework_region\n13 framework_region\n14 framework_region\n15 framework_region\n16 framework_region\n17 framework_region\n18 framework_region\n19 framework_region\n20 framework_region\n21 framework_region\n22 framework_region\n23 framework_region\n24 L1\n25 L1\n26 L1\n27 L1\n28 L1\n29 L1\n30 L1\n31 L1\n32 L1\n33 L1\n34 L1\n35 framework_region\n36 framework_region\n37 framework_region\n38 framework_region\n39 framework_region\n40 framework_region\n41 framework_region\n42 framework_region\n43 framework_region\n44 framework_region\n45 framework_region\n46 framework_region\n47 framework_region\n48 framework_region\n49 L2\n50 L2\n51 L2\n52 L2\n53 L2\n54 L2\n55 L2\n56 L2\n57 framework_region\n58 framework_region\n59 framework_region\n60 framework_region\n61 framework_region\n62 framework_region\n63 framework_region\n64 framework_region\n65 framework_region\n66 framework_region\n67 framework_region\n68 framework_region\n69 framework_region\n70 framework_region\n71 framework_region\n72 framework_region\n73 framework_region\n74 framework_region\n75 framework_region\n76 framework_region\n77 framework_region\n78 framework_region\n79 framework_region\n80 framework_region\n81 framework_region\n82 framework_region\n83 framework_region\n84 framework_region\n85 framework_region\n86 framework_region\n87 framework_region\n88 framework_region\n89 L3\n90 L3\n91 L3\n92 L3\n93 L3\n94 L3\n95 L3\n96 L3\n97 L3\n98 framework_region\n99 framework_region\n100 framework_region\n101 framework_region\n102 framework_region\n103 framework_region\n104 framework_region\n105 framework_region\n106 framework_region\n107 framework_region\n108 framework_region\n109 framework_region\n110 framework_region\n111 framework_region\n112 framework_region\n113 framework_region\n114 framework_region\n115 framework_region\n116 framework_region\n117 framework_region\n118 framework_region\n119 framework_region\n120 framework_region\n121 framework_region\n122 framework_region\n123 framework_region\n124 framework_region\n125 framework_region\n126 framework_region\n127 framework_region\n128 framework_region\n129 framework_region\n130 framework_region\n131 H1\n132 H1\n133 H1\n134 H1\n135 H1\n136 H1\n137 H1\n138 H1\n139 H1\n140 H1\n141 H1\n142 H1\n143 H1\n144 framework_region\n145 framework_region\n146 framework_region\n147 framework_region\n148 framework_region\n149 framework_region\n150 framework_region\n151 framework_region\n152 framework_region\n153 framework_region\n154 framework_region\n155 framework_region\n156 framework_region\n157 framework_region\n158 H2\n159 H2\n160 H2\n161 H2\n162 H2\n163 H2\n164 H2\n165 H2\n166 H2\n167 H2\n168 framework_region\n169 framework_region\n170 framework_region\n171 framework_region\n172 framework_region\n173 framework_region\n174 framework_region\n175 framework_region\n176 framework_region\n177 framework_region\n178 framework_region\n179 framework_region\n180 framework_region\n181 framework_region\n182 framework_region\n183 framework_region\n184 framework_region\n185 framework_region\n186 framework_region\n187 framework_region\n188 framework_region\n189 framework_region\n190 framework_region\n191 framework_region\n192 framework_region\n193 framework_region\n194 framework_region\n195 framework_region\n196 framework_region\n197 framework_region\n198 framework_region\n199 framework_region\n200 framework_region\n201 framework_region\n202 framework_region\n203 framework_region\n204 framework_region\n205 H3\n206 H3\n207 H3\n208 H3\n209 H3\n210 H3\n211 H3\n212 H3\n213 H3\n214 H3\n215 framework_region\n216 framework_region\n217 framework_region\n218 framework_region\n219 framework_region\n220 framework_region\n221 framework_region\n222 framework_region\n223 framework_region\n224 framework_region\n225 framework_region\n226 antigen_region\n227 antigen_region\n228 antigen_region\n229 antigen_region\n230 antigen_region\n231 antigen_region\n232 antigen_region\n233 antigen_region\n234 antigen_region\n235 antigen_region\n236 antigen_region\n237 antigen_region\n238 antigen_region\n239 antigen_region\n240 antigen_region\n241 antigen_region\n242 antigen_region\n243 antigen_region\n244 antigen_region\n245 antigen_region\n246 antigen_region\n247 antigen_region\n248 antigen_region\n249 antigen_region\n250 antigen_region\n251 antigen_region\n252 antigen_region\n253 antigen_region\n254 antigen_region\n255 antigen_region\n256 antigen_region\n257 antigen_region\n258 antigen_region\n259 antigen_region\n260 antigen_region\n261 antigen_region\n262 antigen_region\n263 antigen_region\n264 antigen_region\n265 antigen_region\n266 antigen_region\n267 antigen_region\n268 antigen_region\n269 antigen_region\n270 antigen_region\n271 antigen_region\n272 antigen_region\n273 antigen_region\n274 antigen_region\n275 antigen_region\n276 antigen_region\n277 antigen_region\n278 antigen_region\n279 antigen_region\n280 antigen_region\n281 antigen_region\n282 antigen_region\n283 antigen_region\n284 antigen_region\n285 antigen_region\n286 antigen_region\n287 antigen_region\n288 antigen_region\n289 antigen_region\n290 antigen_region\n291 antigen_region\n292 antigen_region\n293 antigen_region\n294 antigen_region\n295 antigen_region\n296 antigen_region\n297 antigen_region\n298 antigen_region\n299 antigen_region\n300 antigen_region\n301 antigen_region\n302 antigen_region\n303 antigen_region\n304 antigen_region\n305 antigen_region\n306 antigen_region\n307 antigen_region\n308 antigen_region\n309 antigen_region\n310 antigen_region\n311 antigen_region\n312 antigen_region\n313 antigen_region\n314 antigen_region\n315 antigen_region\n316 antigen_region\n317 antigen_region\n318 antigen_region\n319 antigen_region\n320 antigen_region\n321 antigen_region\n322 antigen_region\n323 antigen_region\n324 antigen_region\n325 antigen_region\n326 antigen_region\n327 antigen_region\n328 antigen_region\n329 antigen_region\n330 antigen_region\n331 antigen_region\n332 antigen_region\n333 antigen_region\n334 antigen_region\n335 antigen_region\n336 antigen_region\n337 antigen_region\n338 antigen_region\n339 antigen_region\n340 antigen_region\n341 antigen_region\n342 antigen_region\n343 antigen_region\n344 antigen_region\n345 antigen_region\n346 antigen_region\n347 antigen_region\n348 antigen_region\n349 antigen_region\n350 antigen_region\n351 antigen_region\n352 antigen_region\n353 antigen_region\n354 antigen_region\n355 antigen_region\n356 antigen_region\n357 antigen_region\n358 antigen_region\n359 antigen_region\n360 antigen_region\n361 antigen_region\n362 antigen_region\n363 antigen_region\n364 antigen_region\n365 antigen_region\n366 antigen_region\n367 antigen_region\n368 antigen_region\n369 antigen_region\n370 antigen_region\n371 antigen_region\n372 antigen_region\n373 antigen_region\n374 antigen_region\n375 antigen_region\n376 antigen_region\n377 antigen_region\n378 antigen_region\n379 antigen_region\n380 antigen_region\n381 antigen_region\n382 antigen_region\n383 antigen_region\n384 antigen_region\n385 antigen_region\n386 antigen_region\n387 antigen_region\n388 antigen_region\n389 antigen_region\n390 antigen_region\n391 antigen_region\n392 antigen_region\n393 antigen_region\n394 antigen_region\n395 antigen_region\n396 antigen_region\n397 antigen_region\n398 antigen_region\n399 antigen_region\n400 antigen_region\n401 antigen_region\n402 antigen_region\n403 antigen_region\n404 antigen_region\n405 antigen_region\n406 antigen_region\n407 antigen_region\n408 antigen_region\n409 antigen_region\n410 antigen_region\n411 antigen_region\n412 antigen_region\n413 antigen_region\n414 antigen_region\n415 antigen_region\n416 antigen_region\n417 antigen_region\n418 antigen_region\n419 antigen_region\n420 antigen_region\n421 antigen_region\n422 antigen_region\n423 antigen_region\n424 antigen_region\n425 antigen_region\n426 antigen_region\n427 antigen_region\n428 antigen_region\n429 antigen_region\n430 antigen_region\n431 antigen_region\n432 antigen_region\n433 antigen_region\n434 antigen_region\n435 antigen_region\n436 antigen_region\n437 antigen_region\n438 antigen_region\n439 antigen_region\n440 antigen_region\n441 antigen_region\n442 antigen_region\n443 antigen_region\n444 antigen_region\n445 antigen_region\n446 antigen_region\n447 antigen_region\n448 antigen_region\n449 antigen_region\n450 antigen_region\n451 antigen_region\n452 antigen_region\n453 antigen_region\n454 antigen_region\n455 antigen_region\n456 antigen_region\n457 antigen_region\n458 antigen_region\n459 antigen_region\n460 antigen_region\n461 antigen_region\n462 antigen_region\n463 antigen_region\n464 antigen_region\n11\nCDRClusterEnum.L1_11_1\n7.1372427840879435\n23 H \nResidue 130: CYS:disulfide (CYS, C):\nBase: CYS\n Properties: POLYMER PROTEIN CANONICAL_AA SC_ORBITALS METALBINDING DISULFIDE_BONDED ALPHA_AA L_AA\n Variant types: DISULFIDE\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB SG 1HB 2HB \nAtom Coordinates:\n N : -13.918, -0.011, 40.022\n CA : -15.022, -0.943, 39.837\n C : -16.073, -0.624, 40.895\n O : -15.877, -0.945, 42.066\n CB : -14.515, -2.379, 40.021\n SG : -15.8, -3.608, 40.319\n H : -13.6187, 0.217354, 40.9592\n HA : -15.4065, -0.826975, 38.8236\n 1HB : -13.9648, -2.68746, 39.1317\n 2HB : -13.8236, -2.41565, 40.8626\nMirrored relative to coordinates in ResidueType: FALSE\n\n106 H \nResidue 204: CYS:disulfide (CYS, C):\nBase: CYS\n Properties: POLYMER PROTEIN CANONICAL_AA SC_ORBITALS METALBINDING DISULFIDE_BONDED ALPHA_AA L_AA\n Variant types: DISULFIDE\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB SG 1HB 2HB \nAtom Coordinates:\n N : -14.312, -6.402, 36.316\n CA : -14.452, -6.929, 37.646\n C : -15.678, -7.837, 37.662\n O : -16.599, -7.672, 36.856\n CB : -14.501, -5.824, 38.705\n SG : -15.935, -4.767, 38.638\n H : -14.9281, -5.66132, 36.0129\n HA : -13.5885, -7.5585, 37.8613\n 1HB : -14.4721, -6.27099, 39.699\n 2HB : -13.6222, -5.18697, 38.607\nMirrored relative to coordinates in ResidueType: FALSE\n\nDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKREVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSS\nL1 RASQDVSTAVA\nCDRNameEnum.h1 AASGFTISNSGIH\nCDRNameEnum.h2 WIYPTGGATD\nCDRNameEnum.h3 ARFWWRSFDY\nCDRNameEnum.l1 RASQDVSTAVA\nCDRNameEnum.l2 YSASFLYS\nCDRNameEnum.l3 QQSYTTPPT\nvector1_bool[0, 0, 0, 0, 0, 0]\nLOOP begin end cut skip_rate extended\nLOOP start: 203 stop: 216 cut: 210 size: 14 skip rate: 0 extended?: False\n\nLOOP start: 87 stop: 99 cut: 93 size: 13 skip rate: 0 extended?: False\n\n\n267\n270\n271\n272\n273\n299\n300\n301\n302\n303\n304\n305\n307\n308\n309\n310\n313\n396\n397\n398\n454\n458\nTotal Epitope Residues: 22\n\nSASA 531.9639835627297\n\nTOTAL RESIDUE ENERGY -2.6964334368036424\n\nSELECTION select rosetta_sele, (chain A and resid 42,45,46,47,48,74,75,76,77,78,79,80,82,83,84,85,88,171,172,173,229,233)\n(300, 0.0)\n(303, 0.0)\n(305, 0.0)\n(304, 0.4468042885105504)\n(267, 1.024686682355324)\n(398, 1.8244508447514138)\n(302, 4.098746729421277)\n(396, 4.098746729421277)\n(271, 5.380780270728442)\n(307, 5.504698647620041)\n(301, 7.689850871116937)\n(313, 8.068377879289471)\n(270, 8.322490061360945)\n(458, 14.530261630816586)\n(310, 17.873691916125896)\n(308, 39.92505047193878)\n(454, 46.22431607929343)\n(397, 54.69632267990853)\n(299, 60.31999848338232)\n(309, 75.13475653929288)\n(272, 76.34620896564937)\n(273, 100.45374379174626)\n300 75 A 0.0\n303 78 A 0.0\n305 80 A 0.0\n304 79 A 0.4468042885105504\n267 42 A 1.024686682355324\n398 173 A 1.8244508447514138\n302 77 A 4.098746729421277\n396 171 A 4.098746729421277\n271 46 A 5.380780270728442\n307 82 A 5.504698647620041\n301 76 A 7.689850871116937\n313 88 A 8.068377879289471\n270 45 A 8.322490061360945\n458 233 A 14.530261630816586\n310 85 A 17.873691916125896\n308 83 A 39.92505047193878\n454 229 A 46.22431607929343\n397 172 A 54.69632267990853\n299 74 A 60.31999848338232\n309 84 A 75.13475653929288\n272 47 A 76.34620896564937\n273 48 A 100.45374379174626\n89 107 L \n90 108 L \n91 109 L \n92 110 L \n93 111 L \n94 135 L \n95 136 L \n96 137 L \n97 138 L \n205 107 H \n206 108 H \n207 109 H \n208 110 H \n209 111 H \n210 134 H \n211 135 H \n212 136 H \n213 137 H \n214 138 H \n226 1 A \n227 2 A \n228 3 A \n229 4 A \n230 5 A \n231 6 A \n232 7 A \n233 8 A \n234 9 A \n235 10 A \n236 11 A \n237 12 A \n238 13 A \n239 14 A \n240 15 A \n241 16 A \n242 17 A \n243 18 A \n244 19 A \n245 20 A \n246 21 A \n247 22 A \n248 23 A \n249 24 A \n250 25 A \n251 26 A \n252 27 A \n253 28 A \n254 29 A \n255 30 A \n256 31 A \n257 32 A \n258 33 A \n259 34 A \n260 35 A \n261 36 A \n262 37 A \n263 38 A \n264 39 A \n265 40 A \n266 41 A \n267 42 A \n268 43 A \n269 44 A \n270 45 A \n271 46 A \n272 47 A \n273 48 A \n274 49 A \n275 50 A \n276 51 A \n277 52 A \n278 53 A \n279 54 A \n280 55 A \n281 56 A \n282 57 A \n283 58 A \n284 59 A \n285 60 A \n286 61 A \n287 62 A \n288 63 A \n289 64 A \n290 65 A \n291 66 A \n292 67 A \n293 68 A \n294 69 A \n295 70 A \n296 71 A \n297 72 A \n298 73 A \n299 74 A \n300 75 A \n301 76 A \n302 77 A \n303 78 A \n304 79 A \n305 80 A \n306 81 A \n307 82 A \n308 83 A \n309 84 A \n310 85 A \n311 86 A \n312 87 A \n313 88 A \n314 89 A \n315 90 A \n316 91 A \n317 92 A \n318 93 A \n319 94 A \n320 95 A \n321 96 A \n322 97 A \n323 98 A \n324 99 A \n325 100 A \n326 101 A \n327 102 A \n328 103 A \n329 104 A \n330 105 A \n331 106 A \n332 107 A \n333 108 A \n334 109 A \n335 110 A \n336 111 A \n337 112 A \n338 113 A \n339 114 A \n340 115 A \n341 116 A \n342 117 A \n343 118 A \n344 119 A \n345 120 A \n346 121 A \n347 122 A \n348 123 A \n349 124 A \n350 125 A \n351 126 A \n352 127 A \n353 128 A \n354 129 A \n355 130 A \n356 131 A \n357 132 A \n358 133 A \n359 134 A \n360 135 A \n361 136 A \n362 137 A \n363 138 A \n364 139 A \n365 140 A \n366 141 A \n367 142 A \n368 143 A \n369 144 A \n370 145 A \n371 146 A \n372 147 A \n373 148 A \n374 149 A \n375 150 A \n376 151 A \n377 152 A \n378 153 A \n379 154 A \n380 155 A \n381 156 A \n382 157 A \n383 158 A \n384 159 A \n385 160 A \n386 161 A \n387 162 A \n388 163 A \n389 164 A \n390 165 A \n391 166 A \n392 167 A \n393 168 A \n394 169 A \n395 170 A \n396 171 A \n397 172 A \n398 173 A \n399 174 A \n400 175 A \n401 176 A \n402 177 A \n403 178 A \n404 179 A \n405 180 A \n406 181 A \n407 182 A \n408 183 A \n409 184 A \n410 185 A \n411 186 A \n412 187 A \n413 188 A \n414 189 A \n415 190 A \n416 191 A \n417 192 A \n418 193 A \n419 194 A \n420 195 A \n421 196 A \n422 197 A \n423 198 A \n424 199 A \n425 200 A \n426 201 A \n427 202 A \n428 203 A \n429 204 A \n430 205 A \n431 206 A \n432 207 A \n433 208 A \n434 209 A \n435 210 A \n436 211 A \n437 212 A \n438 213 A \n439 214 A \n440 215 A \n441 216 A \n442 217 A \n443 218 A \n444 219 A \n445 220 A \n446 221 A \n447 222 A \n448 223 A \n449 224 A \n450 225 A \n451 226 A \n452 227 A \n453 228 A \n454 229 A \n455 230 A \n456 231 A \n457 232 A \n458 233 A \n459 234 A \n460 235 A \n461 236 A \n462 237 A \n463 238 A \nH3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.355791 seconds to load from binary\n[NbConvertApp] Converting notebook 12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb to python\n[NbConvertApp] Writing 18559 bytes to 12.01-RosettaAntibody-Framework-and-SimpleMetrics.py\n/bin/sh: 1: pip: not found\n12.01-RosettaAntibody-Framework-and-SimpleMetrics.py:49: 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.select import residue_selector as selections\n", "state": "passed"}, "12.02-RosettaAntibodyDesign-RAbD": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 12.02-RosettaAntibodyDesign-RAbD.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 12.02-RosettaAntibodyDesign-RAbD.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=875906321 seed_offset=0 real_seed=875906321\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=875906321 RG_type=mt19937\ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -no_fconfig @inputs/rabd/common -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2020948121 seed_offset=0 real_seed=-2020948121\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2020948121 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 1.95762 seconds.\ncore.import_pose.import_pose: File 'inputs/rabd/my_ab.pdb' automatically determined to be of type PDB\ncore.io.pdb.pdb_reader: Parsing 993 .pdb records with unknown format to search for Rosetta-specific comments.\ncore.conformation.Conformation: Found disulfide between residues 771 845\ncore.conformation.Conformation: current variant for 771 CYS\ncore.conformation.Conformation: current variant for 845 CYS\ncore.conformation.Conformation: current variant for 771 CYD\ncore.conformation.Conformation: current variant for 845 CYD\ncore.conformation.Conformation: Found disulfide between residues 891 956\ncore.conformation.Conformation: current variant for 891 CYS\ncore.conformation.Conformation: current variant for 956 CYS\ncore.conformation.Conformation: current variant for 891 CYD\ncore.conformation.Conformation: current variant for 956 CYD\nprotocols.rosetta_scripts.RosettaScriptsParser: Validating input script...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...\nprotocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: ...done\nprotocols.rosetta_scripts.RosettaScriptsParser: Parsed script:\n<ROSETTASCRIPTS>\n\t<MOVERS>\n\t\t<AntibodyDesignMover light_chain=\"kappa\" name=\"RAbD\" seq_design_cdrs=\"L1,L3\"/>\n\t</MOVERS>\n\t<PROTOCOLS/>\n</ROSETTASCRIPTS>\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.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\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"RAbD\" of type AntibodyDesignMover\nprotocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings\nbasic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt\nprotocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully\nprotocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully\nantibody.AntibodyInfo: Successfully finished the CDR definition\nantibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type\nantibody.AntibodyInfo: SRWGGDGFYAMDYW\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED\nantibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0\nantibody.AntibodyInfo: Setting up CDR Cluster for H1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for H3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L1\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L2\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT\nantibody.AntibodyInfo: Setting up CDR Cluster for L3\nprotocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT\ncore.energy_methods.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt\ncore.energy_methods.CartesianBondedEnergy: Read 759 bb-independent lengths.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1434 bb-independent angles.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt\ncore.energy_methods.CartesianBondedEnergy: Read 1 bb-independent torsions.\nbasic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt\ncore.energy_methods.CartesianBondedEnergy: Read 529 bb-independent improper tors.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.import_pose.import_pose: File 'malaria_cdrs.pdb' automatically determined to be of type PDB\ncore.io.pdb.pdb_reader: Parsing 0 .pdb records with unknown format to search for Rosetta-specific comments.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 387\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 601\ncore.conformation.Conformation: Found disulfide between residues 8 22\ncore.conformation.Conformation: current variant for 8 CYS\ncore.conformation.Conformation: current variant for 22 CYS\ncore.conformation.Conformation: current variant for 8 CYD\ncore.conformation.Conformation: current variant for 22 CYD\ncore.conformation.Conformation: Found disulfide between residues 24 36\ncore.conformation.Conformation: current variant for 24 CYS\ncore.conformation.Conformation: current variant for 36 CYS\ncore.conformation.Conformation: current variant for 24 CYD\ncore.conformation.Conformation: current variant for 36 CYD\ncore.conformation.Conformation: Found disulfide between residues 43 58\ncore.conformation.Conformation: current variant for 43 CYS\ncore.conformation.Conformation: current variant for 58 CYS\ncore.conformation.Conformation: current variant for 43 CYD\ncore.conformation.Conformation: current variant for 58 CYD\ncore.conformation.Conformation: Found disulfide between residues 52 70\ncore.conformation.Conformation: current variant for 52 CYS\ncore.conformation.Conformation: current variant for 70 CYS\ncore.conformation.Conformation: current variant for 52 CYD\ncore.conformation.Conformation: current variant for 70 CYD\ncore.conformation.Conformation: Found disulfide between residues 72 83\ncore.conformation.Conformation: current variant for 72 CYS\ncore.conformation.Conformation: current variant for 83 CYS\ncore.conformation.Conformation: current variant for 72 CYD\ncore.conformation.Conformation: current variant for 83 CYD\ncore.conformation.Conformation: Found disulfide between residues 88 98\ncore.conformation.Conformation: current variant for 88 CYS\ncore.conformation.Conformation: current variant for 98 CYS\ncore.conformation.Conformation: current variant for 88 CYD\ncore.conformation.Conformation: current variant for 98 CYD\ncore.conformation.Conformation: Found disulfide between residues 93 111\ncore.conformation.Conformation: current variant for 93 CYS\ncore.conformation.Conformation: current variant for 111 CYS\ncore.conformation.Conformation: current variant for 93 CYD\ncore.conformation.Conformation: current variant for 111 CYD\ncore.conformation.Conformation: Found disulfide between residues 113 127\ncore.conformation.Conformation: current variant for 113 CYS\ncore.conformation.Conformation: current variant for 127 CYS\ncore.conformation.Conformation: current variant for 113 CYD\ncore.conformation.Conformation: current variant for 127 CYD\ncore.conformation.Conformation: Found disulfide between residues 135 146\ncore.conformation.Conformation: current variant for 135 CYS\ncore.conformation.Conformation: current variant for 146 CYS\ncore.conformation.Conformation: current variant for 135 CYD\ncore.conformation.Conformation: current variant for 146 CYD\ncore.conformation.Conformation: Found disulfide between residues 139 155\ncore.conformation.Conformation: current variant for 139 CYS\ncore.conformation.Conformation: current variant for 155 CYS\ncore.conformation.Conformation: current variant for 139 CYD\ncore.conformation.Conformation: current variant for 155 CYD\ncore.conformation.Conformation: Found disulfide between residues 157 170\ncore.conformation.Conformation: current variant for 157 CYS\ncore.conformation.Conformation: current variant for 170 CYS\ncore.conformation.Conformation: current variant for 157 CYD\ncore.conformation.Conformation: current variant for 170 CYD\ncore.conformation.Conformation: Found disulfide between residues 197 261\ncore.conformation.Conformation: current variant for 197 CYS\ncore.conformation.Conformation: current variant for 261 CYS\ncore.conformation.Conformation: current variant for 197 CYD\ncore.conformation.Conformation: current variant for 261 CYD\ncore.conformation.Conformation: Found disulfide between residues 307 367\ncore.conformation.ConformPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nation: current variant for 307 CYS\ncore.conformation.Conformation: current variant for 367 CYS\ncore.conformation.Conformation: current variant for 307 CYD\ncore.conformation.Conformation: current variant for 367 CYD\ncore.conformation.Conformation: Found disulfide between residues 407 481\ncore.conformation.Conformation: current variant for 407 CYS\ncore.conformation.Conformation: current variant for 481 CYS\ncore.conformation.Conformation: current variant for 407 CYD\ncore.conformation.Conformation: current variant for 481 CYD\ncore.conformation.Conformation: Found disulfide between residues 527 582\ncore.conformation.Conformation: current variant for 527 CYS\ncore.conformation.Conformation: current variant for 582 CYS\ncore.conformation.Conformation: current variant for 527 CYD\ncore.conformation.Conformation: current variant for 582 CYD\n[NbConvertApp] Converting notebook 12.02-RosettaAntibodyDesign-RAbD.ipynb to python\n[NbConvertApp] Writing 48375 bytes to 12.02-RosettaAntibodyDesign-RAbD.py\n/bin/sh: 1: pip: not found\n12.02-RosettaAntibodyDesign-RAbD.py:168: 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.rosetta_scripts import *\n", "state": "passed"}, "13.00-RosettaCarbohydrates-Working-with-Glycans": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 13.00-RosettaCarbohydrates-Working-with-Glycans.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=489166636 seed_offset=0 real_seed=489166636\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=489166636 RG_type=mt19937\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -include_sugars -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-563785258 seed_offset=0 real_seed=-563785258\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-563785258 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 3.07758 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.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 'inputs/glycans/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 'inputs/glycans/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 'inputs/glycans/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 'inputs/glycans/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::atoPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nmaltotriose\n PDB 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 \n\nisomaltose\n PDB file name: alpha-D-Glcp-(1->6)-alpha-D-Glcp\nTotal residues: 2\nSequence: ZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 \n\nlactose\n PDB 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\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\n(1, 120)\n(2, 60)\n(3, 60)\n(4, 0)\n(5, 60)\n44.32677030464958\n-170.86933817075462\n49.383018645410004\n59.99999999999999\n-59.99999999999999\n60.00000000000001\n300.0\n59.999999999999986\n4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\nPDB file name: inputs/glycans/Lex.pdb\nTotal residues: 3\nSequence: ZZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 EDGE 1 3 -2 O3 C1 \nPDB file name: inputs/glycans/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-\nm_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 'inputs/glycans/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[NbConvertApp] Converting notebook 13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb to python\n[NbConvertApp] Writing 33499 bytes to 13.00-RosettaCarbohydrates-Working-with-Glycans.py\n/bin/sh: 1: pip: not found\n", "state": "passed"}, "13.01-Glycan-Trees-Selectors-and-Movers": {"log": "cd /home/benchmark/working_dir/notebooks && /home/benchmark/working_dir/.python_virtual_environment/bin/python -m nbconvert --to python 13.01-Glycan-Trees-Selectors-and-Movers.ipynb && export DEBUG=\"DEBUG\" && /home/benchmark/rosetta/source/test/timelimit.py 12 /home/benchmark/working_dir/.python_virtual_environment/bin/ipython --HistoryManager.enabled=False 13.01-Glycan-Trees-Selectors-and-Movers.py\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=578520415 seed_offset=0 real_seed=578520415\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=578520415 RG_type=mt19937\ncore.init: Rosetta version: 2022.35.post.dev+12.HEAD.f8d1edff335 f8d1edff335ebf0332099034afcf88331ae302e0 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-09-14T18:40:19\ncore.init: command: PyRosetta -ignore_unrecognized_res -include_sugars -auto_detect_glycan_connections -maintain_links -alternate_3_letter_codes pdb_sugar -write_glycan_pdb_codes -ignore_zero_occupancy false -load_PDB_components false -no_fconfig -database /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=179742142 seed_offset=0 real_seed=179742142\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=179742142 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 2.95821 seconds.\ncore.import_pose.import_pose: File 'inputs/glycans/4do4_refined.pdb' automatically determined to be of type PDB\ncore.io.util: Found 18 glycan linkages in the structure based on atomic distances\ncore.io.util: Automatic glycan connection is activated.\ncore.io.util: Start reordering residues.\ncore.io.util: Corrected glycan residue order (internal numbering): [388, 389, 390, 391, 392, 393, 394, 395, 396, 797, 798, 799, 800, 801, 802, 803, 804, 805]\ncore.io.util: \ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 390\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 394\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 395\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 396\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 798\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 799\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 803\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Setting chain termination for 804\ncore.io.util: Found 18 glycan linkages in the structure based on atomic distances\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc388 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc389 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man390 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc391 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc392 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man393 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man394 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man395 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc396 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc797 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc798 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Fuc799 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc800 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc801 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man802 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man803 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man804 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc805 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 387\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue HIS:CtermProteinFull 796\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 388. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 391. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:non-reducing_end 395. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:->6)-branch:2-AcNH 797. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-L-Fucp:non-reducing_end 799. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 800. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:non-reducing_end 804. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805. Returning BOGUS ID instead.\ncore.conformation.Conformation: Found disulfide between residues 21 63\ncore.conformation.Conformation: current variant for 21 CYS\ncore.conformation.Conformation: current variant for 63 CYS\ncore.conformation.Conformation: current variant for 21 CYD\ncore.conformation.Conformation: current variant for 63 CYD\ncore.conformation.Conformation: Found disulfide between residues 417 459\ncore.conformation.Conformation: current variant for 417 CYS\ncore.conformation.Conformation: current variant for 459 CYS\ncore.conformation.Conformation: current variant for 417 CYD\ncore.conformation.Conformation: current variant for 459 CYD\ncore.conformation.Conformation: Found disulfide between residues 25 32\ncore.conformation.Conformation: current variant for 25 CYS\ncore.conformation.Conformation: current variant for 32 CYS\ncore.conformation.Conformation: current variant for 25 CYD\ncore.conformation.Conformation: current variant for 32 CYD\ncore.conformation.Conformation: Found disulfide between residues 421 428\ncore.conformation.Conformation: current variant for 421 CYS\ncore.conformation.Conformation: current variant for 428 CYS\ncore.conformation.Conformation: current variant for 421 CYD\ncore.conformation.Conformation: current variant for 428 CYD\ncore.conformation.Conformation: Found disulfide between residues 110 141\ncore.conformation.Conformation: current variant for 110 CYS\ncore.conformation.Conformation: current variant for 141 CYS\ncore.conformation.Conformation: current variant for 110 CYD\ncore.conformation.Conformation: current variant for 141 CYD\ncore.conformation.Conformation: Found disulfide between residues 506 537\ncore.conformation.Conformation: current variant for 506 CYS\ncore.conformation.Conformation: current variant for 537 CYS\ncore.conformation.Conformation: current variant for 506 CYD\ncore.conformation.Conformation: current variant for 537 CYD\ncore.conformation.Conformation: Found disulfide between residues 170 192\ncore.conformation.Conformation: current variant for 170 CYS\ncore.conformation.Conformation: current variant for 192 CYS\ncore.conformation.Conformation: current variant for 170 CYD\ncore.conformation.Conformation: current variant for 192 CYD\ncore.conformation.Conformation: Found disulfide between residues 566 588\ncore.conformation.Conformation: current variant for 566 CYS\ncore.conformation.Conformation: current variant for 588 CYS\ncore.conformation.Conformation: current variant for 566 CYD\ncore.conformation.Conformation: current variant for 588 CYD\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 6 glycan trees.\nBranch Point: ASN 107 124 A \nBranch Point: ASN 160 177 A \nBranch Point: ASN 368 385 A \nCarbohydrate: 388 501 A Parent: 107 BP: 0 501 A CON: _->4 DIS: 0 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 389 502 A Parent: 388 BP: 0 502 A CON: _->4 DIS: 1 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 390 503 A Parent: 389 BP: 0 503 A CON: DIS: 2 ShortName: beta-D-Manp-\nCarbohydrate: 391 504 A Parent: 160 BP: 0 504 A CON: _->4 DIS: 0 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 392 505 A Parent: 391 BP: 0 505 A CON: _->4 DIS: 1 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 393 506 A Parent: 392 BP: 1 506 A CON: _->3,_->6 DIS: 2 ShortName: ->3)-beta-D-Manp-\nCarbohydrate: 394 507 A Parent: 393 BP: 0 507 A CON: DIS: 3 ShortName: alpha-D-Manp-\nCarbohydrate: 395 508 A Parent: 393 BP: 0 508 A CON: DIS: 3 ShortName: alpha-D-Manp-\nCarbohydrate: 396 509 A Parent: 368 BP: 0 509 A CON: DIS: 0 ShortName: beta-D-GlcpNAc-\nBranch Point: ASN 503 124 B \nBranch Point: ASN 556 177 B \nBranch Point: ASN 764 385 B \nCarbohydrate: 797 501 B Parent: 503 BP: 1 501 B CON: _->4,_->6 DIS: 0 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 798 502 B Parent: 797 BP: 0 502 B CON: DIS: 1 ShortName: beta-D-GlcpNAc-\nCarbohydrate: 799 503 B Parent: 797 BP: 0 503 B CON: DIS: 1 ShortName: alpha-L-Fucp-\nCarbohydrate: 800 504 B Parent: 556 BP: 0 504 B CON: _->4 DIS: 0 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 801 505 B Parent: 800 BP: 0 505 B CON: _->4 DIS: 1 ShortName: ->4)-beta-D-GlcpNAc-\nCarbohydrate: 802 506 B Parent: 801 BP: 1 506 B CON: _->3,_->6 DIS: 2 ShortName: ->3)-beta-D-Manp-\nCarbohydrate: 803 507 B Parent: 802 BP: 0 507 B CON: DIS: 3 ShortName: alpha-D-Manp-\nCarbohydrate: 804 508 B Parent: 802 BP: 0 508 B CON: DIS: 3 ShortName: alpha-D-Manp-\nCarbohydrate: 805 509 B Parent: 764 BP: 0 509 B CON: DIS: 0 ShortName: beta-D-GlcpNAc-\nGlycan Residues: 18\nProtein BPs: 6\nTREES\n107 124 A Length: 3\n160 177 A Length: 5\n368 385 A Length: 1\n503 124 B Length: 3\n556 177 B Length: 5\n764 385 B Length: 1\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Use ResidueInSequenceMotifSelector with regular expression \ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKZZZZZZZZZLDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NFT) at sequence position 107\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: FTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKZZZZZZZZZLDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NAT) at sequence position 160\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: ATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKZZZZZZZZZLDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NFT) at sequence position 342\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: FTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKZZZZZZZZZLDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NFT) at sequence position 368\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: FTVIINPSGVVMWYLYPIKZZZZZZZZZLDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NFT) at sequence position 503\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: FTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NAT) at sequence position 556\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: ATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NFT) at sequence position 738\ncore.select.residue_selector.ResidueInSequenceMotifSelector: searching in: FTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHHZZZZZZZZZ\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found motif (NFT) at sequence position 764\ncore.select.residue_selector.ResidueInSequenceMotifSelector: Found 8 motifs in sequence.\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: The -include_sugars flag was used with no sugar_bb weight set in the weights file. Setting sugar_bb weight to 0.5 by default.\ncore.scoring.ScoringManager: Creating CHI Energy Function.\ncore.scoring.carbohydrates.CHIEnergyFunction: Setting up chi sampling\ncore.scoring.ScoringManager: Creating carbohydrate omega preferences function.\ncore.scoring.carbohydrates.OmegaPreferencesFunction: Setting up omega preference sampling\ncore.scoring.ScoreFunctionFactory: The -include_sugars flag was used without fa_intra_rep_xover4 term in the scorefunction. Setting this term's weight to 0.55. It is generally recommended to use the -beta scorefunction (Rosetta-ICO) with sugars, which includes this and other desired terms such as those bridging waters\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: /home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/working_dir/.python_virtual_environment/lib/python3.7/site-packages/pyrosetta-2022.35.post0.dev0+12.head.f8d1edff335-py3.7-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.285487 seconds to load from binary\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydratesPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\nPyRosetta-4 2022 [Rosetta devel 2022.35.post.dev+12.HEAD.f8d1edff335ebf0332099034afcf88331ae302e0 2022-09-14T18:40:19] retrieved from: git@github.com:CyrusBiotechnology/rosetta-main.git\n(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n6\n5\n388 501 A Glc ->4)-beta-D-Glcp:2-AcNH\n391 504 A Glc ->4)-beta-D-Glcp:2-AcNH\n396 509 A Glc ->3)-beta-D-Glcp:non-reducing_end:2-AcNH\n797 501 B Glc ->4)-beta-D-Glcp:->6)-branch:2-AcNH\n800 504 B Glc ->4)-beta-D-Glcp:2-AcNH\n805 509 B Glc ->3)-beta-D-Glcp:non-reducing_end:2-AcNH\n107 124 A ASN\n160 177 A ASN\n368 385 A ASN\n503 124 B ASN\n556 177 B ASN\n764 385 B ASN\nlength 3\nroot 107\n388 Glc ->4)-beta-D-Glcp:2-AcNH\n389 Glc ->4)-beta-D-Glcp:2-AcNH\n390 Man ->3)-beta-D-Manp:non-reducing_end\nn_children 0\nparent 389\ndistance 2\nexocylic_connection False\nlen 5\nchildren vector1_unsigned_long[803, 804]\nexocyclic False\nexo_803 False\nexo_804 True\n556 ASN\nIs Branch Point: True\n388 Glc\n389 Glc\n390 Man\n391 Glc\n392 Glc\n393 Man\n394 Man\n395 Man\n396 Glc\n797 Glc\n798 Glc\n799 Fuc\n800 Glc\n801 Glc\n802 Man\n803 Man\n804 Man\n805 Glc\n800 Glc\n801 Glc\n802 Man\n803 Man\n804 Man\n800 Glc\n801 Glc\n802 Man\n803 Man\n804 Man\n388 Glc\n389 Glc\n391 Glc\n392 Glc\n396 Glc\n797 Glc\n798 Glc\n799 Fuc\n800 Glc\n801 Glc\n805 Glc\n390 Man\n393 Man\n394 Man\n395 Man\n802 Man\n803 Man\n804 Man\n107 ASN\n160 ASN\n342 ASN\n368 ASN\n503 ASN\n556 ASN\n738 ASN\n764 ASN\n802 Man\n803 Man\n804 Man\n804 Man\n802 Man\n803 Man\n804 Man\n803 Man\n-2470.573838473993 False\n-1251.7050741830603 False\n-1503.5453415266288 False\n-2473.0169704326822 False\n-1051.1615132702063 False\n-2377.998026811734 False\n-16.423575014498383 False\n-1710.672915471789 False\n-2452.417698363766 False\n-2411.414957466861 False\n-1666.4259781545493 False\n-2455.9403036662843 False\n-2186.0204842933945 False\n-2525.5169304429696 False\n-2576.170677883652 False\n3622.314333207015 False\n-2083.91623934 False\n-2336.9897001400564 False\n556.3964761723997 False\n-2411.125174209186 False\n-1244.0214337621965 False\n-209.8510150784807 False\n3441.3881539451227 False\n-2589.0271254236004 False\n-2296.235492659944 False\n-2297.0586432764253 False\n898.7034313878852 False\n-2317.8421029828824 False\n-2387.7409288154995 False\n-2563.5894094677355 False\n314.9110316198905 False\n-1800.572337287745 False\n-2548.813339447679 False\n-1741.2037850830002 False\n-2087.597690188936 False\n-2596.4805531856314 True\n-1531.3305996091144 False\n-2496.194563893436 False\n-2486.1675964065757 False\n205.6039485047193 False\n-2581.25879813956 False\n-1003.3541737692243 False\n-1736.697279886224 False\n-2015.618699275642 False\n-2595.3878459395164 True\n-2036.9277282620242 False\n-2425.5019294518706 False\n-997.5015643836751 False\n-2534.0835262502883 False\n-2406.3848912661133 False\n-2393.895609112199 False\n-2593.0252694402343 True\n-1015.6608766059686 False\n148.26122728759987 False\n-2500.4101339792765 False\n-2552.3854393359734 False\n-2059.8260952092633 False\n-2438.9778578383507 False\n-2006.1745115794824 False\n-2589.186225089671 True\n-2504.885732741377 False\n-2489.8821880364117 False\n-1930.321880335841 False\n-2585.347923003871 False\n-2455.179202584016 False\n-2501.16789395209 False\n-1066.2004279318858 False\n-1369.1482385574636 False\n-2360.1841277084677 False\n-2506.0424867305514 False\n-2509.8784086656574 False\n3001.600872922985 False\n397.5554471436941 False\n-2431.062864320242 False\n-2587.0133803837375 True\n-2495.7137782326763 False\n-2511.9230080908424 False\n-1982.9179855418834 False\n-131.33134913224188 False\n-2006.596632969828 False\n-2578.83062758891 False\n-177.87990425487018 False\n-1639.0843939032152 False\n-2273.254812253904 False\n-2418.295028359109 False\n-1373.767675625019 False\n-2560.727815409892 False\n2177.8415464726404 False\n-2584.2356060519787 False\n-2509.3978297073 False\n-2084.924418860591 False\n-2090.482303020335 False\n-2558.3236630973856 False\n-2002.0005482806555 False\n-2561.877297798064 False\n386.6423034188572 False\n-1533.4751778468371 False\n-2470.2822879449764 False\n-2443.0446128774715 False\n-2140.1556779969005 False\n1223.39415031627 False\n-1785.4423532408873 False\n-2533.68404195427 False\n-2024.4704013619635 False\n-2481.1032470707364 False\n-1779.2064176444946 False\n-2499.5408563812052 False\n-876.6057199096138 False\n554.3664206979325 False\n-2294.1719810496843 False\n2411.8834227632924 False\n-825.9467555224909 False\n-1836.1366255420994 False\n-2136.5101414498504 False\n-1365.7698286375826 False\n-1048.4433636386175 False\n-2292.171126383877 False\n-2576.764999043134 False\n-1266.17910797497 False\n-2583.9376355488484 True\n-2375.7745691629484 False\n-2578.4838644170845 True\n-1815.427421274212 False\n-2537.21292467507 False\n-2508.926489500642 False\n-2113.725373968324 False\n-1429.1767384244986 False\n-2442.5156351332594 False\n-291.8131286843512 False\n-2305.4379353684703 False\n-961.5014821640674 False\n-1878.5273941049704 False\n-2509.6084278552867 False\n-2312.1910736219056 False\n-2488.752682074754 False\n-2205.67201263107 False\n-2500.8311564760124 False\n-2168.2766875361963 False\n3182.309843227875 False\n-241.06665102862365 False\n-2437.0767229102717 False\n-2579.6691853324173 True\n-2451.71496207742 False\n-2520.9125274530434 False\n-2275.2490196993963 False\n-809.7228039909893 False\n-1651.0647525043682 False\n-2517.8908678690937 False\n-1782.8485651929227 False\n-2554.2498881461884 False\n-1374.7736205840456 False\n3395.0978022373347 False\n-1560.7451253848972 False\n-2434.72255300442 False\n-2556.3738543627496 False\n-1223.6174476145288 False\n1585.6591618145003 False\n-2553.264797743364 False\n129.1419730744145 False\n-533.3259472800213 False\n-1765.7528510114098 False\n-2564.30235057434 False\n-1739.6432992383016 False\n-2495.0727728288 False\n-1642.709099586537 False\n-396.63077638764724 False\n-2452.2484323318886 False\n-1751.7539235184672 False\n-2389.8934967251357 False\n-2210.8196109341457 False\n3282.0826202029994 False\n-2295.244892954162 False\n2380.9461827083505 False\n-2550.534762680118 False\n-1717.7790341358082 False\n-2317.0643800827256 False\n-2431.519824237608 False\n-2545.485064834931 False\n-1858.2900913275475 False\n-1561.6399290787722 False\n-2577.8978805381525 True\n-2501.8445088756175 False\n695.0304736011527 False\n-2523.4302112413066 False\n-2241.634387447816 False\n368.94432331825897 False\n1093.762203730725 False\n-1503.2765788645902 False\n-2464.4977254888327 False\n-2307.0009006988626 False\n-281.93238723678826 False\n-2415.476298282107 False\n-2576.8194790387165 False\n-905.1979663040704 False\n-2484.3607519491975 False\n-2340.442494934763 False\n-2539.2763968031986 False\n-2139.371710561607 False\n-2535.3311344127706 False\n-1507.922110512387 False\n-2545.449505823247 False\n-2079.2759819647613 False\n1747.5841615000973 False\n-2.0412022078044316 False\n-2571.956398872291 False\n-2432.9443429652392 False\n-1276.0136239444041 False\n-2364.298721810621 False\n-2564.401387014629 True\n-2465.413557918516 False\n572.8086795122028 False\n-2525.16448523708 False\n-2552.4222598541387 True\n-1858.68583154735 False\n-2507.79272347682 False\n-2537.5757759362778 False\n-2503.4652635669017 False\n-2559.070250125026 True\n-2319.2135515973596 False\n-2554.82929845578 True\n-2550.1987970972527 False\n1546.806142237243 False\n-2331.7214756198687 False\n-2555.1344097491833 True\n-944.5839011189165 False\n-2549.504761589786 False\n-1999.3674001743839 False\n-688.4989044504855 False\n-2506.755968546446 False\n-2526.6022544688717 False\n-1932.2208452461246 False\n-2307.221902808463 False\n-1879.2760877725136 False\n852.5170057459455 False\n-1615.6978013208036 False\n-1294.4580449520913 False\n-2555.986829535515 True\n-2452.072117347925 False\n-2525.8175959134737 False\n-2505.9511486377346 False\n-1611.2356442051478 False\n-2295.3777856803285 False\n5001.436370368714 False\n-2195.0041505357285 False\n329.9132113856237 False\n-2556.346853943039 True\n-2468.3455213927605 False\n-1727.6138453078988 False\n1716.2293691661584 False\n1037.6271462240152 False\n-2084.003893583058 False\n-1149.7719771847933 False\n-929.9801670560689 False\n336.14396551822693 False\n-1618.3134217152287.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D- False\n-2557.5407022350073 True\n-2359.124310090763 False\n-2411.7301133531882 False\n-2548.686762825621 False\n-2556.473605799913 True\n-2546.6448144253745 False\n395.69003406262345 False\n-2499.8942514003625 False\n-2336.427659727596 False\n-1877.2532501145747 False\n-2431.396550200533 False\n-61.30986612679696 False\n-1889.7619551300104 False\n-305.7206880060927 False\n-751.4067622208764 False\n-716.1029804070921 False\n346.3793783440782 False\n-2467.8755493408703 False\n-2315.381389680182 False\n-1846.2505589889624 False\n2532.793209439508 False\n-50.62261764784465 False\n-2563.366922860796 True\n-2281.482772013032 False\n-2558.660922558665 False\n-2515.912872402277 False\n-2549.395070951727 False\n-1970.0401568933976 False\n-2378.7380171438954 False\n-2454.5143255234866 False\n-2090.8259011470504 False\n-722.4901106903039 False\n-1393.1145889530048 False\n-1796.6052691184414 False\n-2568.123729802956 True\n-2547.8870654928983 False\n-2354.385873314078 False\n-1233.0636101690957 False\n-2548.693787134319 False\n-2405.355824619557 False\n-2026.3176695833836 False\n-2385.4205795641997 False\n-2150.4681754056833 False\n-2542.639919716349 False\n-1651.7643992697535 False\n-2365.5097162046204 False\n1076.9379721974415 False\n447.43068409964604 False\n-76.92395329887356 False\n-2103.1084373476624 False\n-2563.7122105410485 True\n-2537.0064832860426 False\n-2565.6436422994107 True\n-1882.2241240083408 False\n-1345.0690136972526 False\n-236.51500129394498 False\n331.8782631109528 False\n-1786.3182429964486 False\n-2436.0448360903565 False\n-2527.725808348354 False\n-2101.4292715279 False\n-2268.9492432710476 False\n-1899.839821562578 False\n16.893849810601594 False\n-2346.192586273704 False\n-2488.7269799362657 False\n-2525.461657468173 False\n-1918.6451835158373 False\n-2444.9680993545544 False\n-2487.0476784345583 False\n-2480.5509834478635 False\n-2232.7052542801584 False\n-2564.8712574344827 True\n-2486.5600258399418 False\n-681.8152645880871 False\n-2064.1431801055255 False\n-2501.6929336007593 False\n-2149.309567000831 False\n-2556.4558733933713 False\n-2520.0398420016686 False\n-1320.020728385401 False\n-2268.0403690925277 False\n6033.958314845321 False\n-2282.155088776865 False\n-2561.6846114923874 False\n-1911.786190087309 False\n7013.166739098047 False\n-2567.664760414655 True\n-2537.8126884898197 False\n-1129.7049267934049 False\n-2311.845610524596 False\n-2550.6029592533655 False\n-2278.2950965380896 False\n-2497.6258048610744 False\n-2092.5010490311 False\n1196.9943700563695 False\n-1345.3015296590656 False\n-2395.053403029423 False\n-2241.8644580875116 False\n-1325.3001421268268 False\n-1228.885478794447 False\n-2517.390673565983 False\n-1432.029326432637 False\n-1383.0685948363316 False\n-2535.2816482686276 False\n-2379.1253701049523 False\n-1898.2765287836546 False\n-2378.7010093091326 False\n99.30460993463689 False\n-2533.129011045395 False\n-2546.4790711388437 False\n-2116.9730728181935 False\n-1385.2858919988012 False\n-191.87792685407055 False\n65.71618780019367 False\n-1297.1971036828804 False\n-2279.7073194985956 False\n-2535.7391089055245 False\n-2477.011479534002 False\n-892.179720136346 False\n-1840.970767124793 False\n3622.6356147319975 False\n-1784.3376218904928 False\n-1183.9633953130233 False\n-2518.00632016581 False\n-2144.787482328935 False\n-2245.389463824583 False\n-2487.7266263586703 False\n-2096.682202514518 False\n-2452.2811260245485 False\n-1371.5549039893644 False\n-2480.9095621312545 False\n-2373.7792863583877 False\n-1607.1188168573358 False\n-2521.6831507076413 False\n-2510.4175516748082 False\n-2547.2323205290954 False\n-2494.389294567735 False\n-2450.907252691921 False\n-1642.7049282663224 False\n-2323.573079040509 False\n-2516.3397630977297 False\n-1737.0035561066393 False\n3936.685114985859 False\n-1367.7323921980378 False\n-2547.0616603186177 False\n2613.4661185847317 False\n1764.924353971046 False\n-2515.564771475704 False\n-1580.9565878032085 False\n-1945.2111464429472 False\n-2413.528558471478 False\n-1644.962635477188 False\n-338.8572668757811 False\n-1121.8206568593537 False\n-2448.963052653657 False\n-2121.6051790156152 False\n-2460.1243891668337 False\n-2258.228876189624 False\n-2537.959402804496 False\n-2467.132782849213 False\n-2508.174817953099 False\n-2565.5350415653893 True\n-2263.590826479127 False\n-2555.9445839611003 False\n-2546.8841057724785 False\n-2287.204460135475 False\n-2476.132747282495 False\n-2416.8489786448454 False\n-2470.3162936055814 False\n-2563.713890533799 True\n-594.33207142518 False\n-2439.8096100561575 False\n-2425.396025164674 False\n551.0801495174867 False\n-1230.1516122657026 False\n-1186.7080038559793 False\n-2568.0066382815708 True\n-2070.963835962797 False\n-1898.766299049702 False\n-2135.0239472059166 False\n-2511.611955983297 False\n2282.731209478789 False\n-2451.8943666282685 False\n1402.8742837916948 False\n-1726.6984946702105 False\n-2552.872495478312 False\n-2492.1095712780566 False\n864.0853226984395 False\n-2551.863287261847 False\n1099.0626012657535 False\n-1066.186269709909 False\n-793.131004315278 False\n-1439.4299042602602 False\n-2344.43012124698 False\n-2226.8504668779883 False\n1403.7698108376921 False\n-2533.32617455926 False\n-2409.724809307916 False\n-2350.018863730453 False\n-2503.173482833534 False\n3818.8729819771575 False\n2595.6008268729643 False\n-2458.430009264594 False\n-2555.298606372783 True\n-1164.8358924463369 False\n-2459.9551827202818 False\n-2555.9566253761695 True\n-865.4115391685882 False\n-2422.299053498612 False\n-2555.549277417145 True\n1535.638157623136 False\n-1688.123039356807 False\n-2481.945519016795 False\n1426.3273671086813 False\n-2504.961847250331 False\n-2277.0921053098286 False\n-1184.5446841541834 False\n-2430.319576891491 False\n6252.007432550204 False\n4386.957443255397 False\n-2537.5480883968976 False\n169.1834657472777 False\n-2473.535424861736 False\n-1381.1703773984987 False\n-2360.856702382099 False\n-2125.8289723662065 False\n-2232.4944047962276 False\n-2526.5141932973706 False\n-2517.52942521644 False\n-2535.4264467480853 False\n43.86905912911435 False\n-2263.0414317923082 False\n-333.6922505680955 False\n-2518.681391266747 False\n-2525.298835736575 False\n-2172.161046461826 False\n-2525.2533531147865 False\n-2405.0513512847842 False\n-2012.4283378433024 False\n-2419.2388909200804 False\n-2544.4522461559427 False\n-2162.1626374525786 False\n-2354.351964522541 False\n-824.9003067626398 False\n-2538.87599371572 False\n-2553.249253982386 True\n-276.2956196011865 False\n-2346.166193819095 False\n1445.9738167391142 False\n2351.269389696434 False\n-2518.0459650541225 False\n-1842.286410039775 False\n-1089.4899101956507 False\n-2497.997447538648 False\n-2273.821057018553 False\n-2463.571566319707 False\n2254.557046260788 False\n-1685.2799203033805 False\n4739.418159250734 False\n-858.750962229047 False\n-1509.4307369666712 False\n-2483.7875281706847 False\n-2107.851867272457 False\n1639.2523188030505 False\n-2429.6067812536276 False\n-1975.7471684838401 False\n238.691146179476 False\n-1827.106446321358 False\n4368.5271835762005 False\n-2450.1151032680946 False\n-2549.3950351849894 False\n-2524.0601219539003 False\n-2551.1234719127456 False\n-1322.6376392116226 False\n-2168.0714923760224 False\n-1266.1314018254711 False\n-2501.1713224883024 False\n497.30809551791924 False\n-2550.7239935084435 False\n-2402.510177132835 False\n1073.4929248904905 False\n1091.1745223895364 False\n-1611.0796800022767 False\n-1280.5568860375092 False\n-1456.8167915146441 False\n-2538.9064902269592 False\n-2364.620594943512 False\n-1866.7414778087332 False\n-2485.3663144280586 False\n-2526.767221980969 False\n-2347.8183525009085 False\n-2132.0547065314786 False\n-549.7043303730863 False\n-457.42014415400024 False\n-1735.2743559289588 False\n-2245.3921063903085 False\n-1790.2600742739642 False\n-2545.3252122379417 False\n-2157.3782228413274 False\n-2552.360443758973 True\n-1119.4032714343248 False\n-2509.144228912728 False\n-2519.2909492353956 False\n-2502.8875996880797 False\n-2516.8328050275645 False\n-2302.985251811246 False\n-2546.408894136945 False\n-2407.075364284013 False\n-2261.040842337955 False\n-475.94199624410135 False\n707.9859151119501 False\n177.73929361325895 False\n-2344.2928762159872 False\n-1236.1370006619527 False\n24.007145696784917 False\n-1927.6151760712396 False\n-2568.4753452680875 True\n-2472.3526402051916 False\n-2520.857162509934 False\n-2474.68150911088 False\n-2537.098699854872 False\n-2575.0071592542317 True\n-2181.98915733523Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling ->3)-beta-D-Manp-(?->4)-beta-D-GlcpNAc- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 0.5599\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->6)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 2 which has a population of 0.4401\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.LinkageConformerMover: Sampling alpha-D-Manp-(?->3)-beta-D-Manp- linkage \nprotocols.carbohydrates.LinkageConformerMover: Sampling conformer 1 which has a population of 1\nprotocols.carbohydrates.LinkageConformerMover: Complete\nprotocols.carbohydrates.TautomerizeAnomerMover: Mover name: TautomerizeAnomerMover, Mover type: TautomerizeAnomerMover, Mover current tag:NoTag\nprotocols.carbohydrates.TautomerizeAnomerMover: Getting movable residues....\nprotocols.carbohydrates.TautomerizeAnomerMover: [ WARNING ] There are no movable residues available in the given pose.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 389\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 389\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 389\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 389\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 389\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 392\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of a terminal residue off residue 0\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 801\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 388 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 389 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Manp:non-reducing_end 390 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 391 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 392 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 394 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 395 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 396 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 798 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-L-Fucp:non-reducing_end 799 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 800 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->4)-beta-D-Glcp:2-AcNH 801 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 803 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-alpha-D-Manp:non-reducing_end 804 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Checking if ->3)-beta-D-Glcp:non-reducing_end:2-AcNH 805 can flip....\nprotocols.carbohydrates.RingPlaneFlipMover: Applying RingPlaneFlipMover to pose....\nprotocols.carbohydrates.RingPlaneFlipMover: Flipping ring plane of residue 389\nprotocols.carbohydrates.RingPlaneFlipMover: Move(s) complete.\nprotocols.carbohydrates.RingPlaneFlipMover: Mover name: RingPlaneFlipMover, Mover type: RingPlaneFlipMover, Mover current tag:NoTag\nprotocols.carbohydrates.RingPlaneFlipMover: Getting movable torsions....\nprotocols.carboh