{"tests": {"C001_Carbohydrates_Demo01": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -constant_seed -include_sugars -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 10.8992 seconds.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/maltotriose.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/isomaltose.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose: by appending by jump...\ncore.conformation.Conformation: appending residue by a chemical bond in the foldtree: 3 ->4)-alpha-L-Fucp:non-reducing_end anchor: O3 1 root: C1 \ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/Lex.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfrPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp\nTotal residues: 3\nSequence: ZZZ\nFold tree:\nFOLD_TREE EDGE 1 3 -1 \nPDB file name: alpha-D-Glcp-(1->6)-alpha-D-Glcp\nTotal residues: 2\nSequence: ZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 \nPDB file name: beta-D-Galp-(1->4)-alpha-D-Glcp\nTotal residues: 2\nSequence: ZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 \nalpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp\nalpha-D-Glcp-(1->6)-alpha-D-Glcp\nbeta-D-Galp-(1->4)-alpha-D-Glcp\n1 ->4)-alpha-D-Glcp:reducing_end\n2 ->4)-beta-D-Galp:non-reducing_end\n1 ->4)-alpha-D-Glcp:reducing_end\n2 ->4)-alpha-D-Glcp\n3 ->4)-alpha-D-Glcp:non-reducing_end\nResidue 1: ->4)-alpha-D-Glcp:reducing_end:non-reducing_end (Glc, Z):\nBase: ->4)-alpha-D-Glcp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: glucose\n IUPAC Name: alpha-D-glucopyranose\n Abbreviation: alpha-D-Glcp\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n none\n Polymeric Information:\n Reducing?: yes\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : axial\n O2 : equatorial\n O3 : equatorial\n O4 : equatorial\n C6 : equatorial\nAtom Coordinates:\n C1 : 0, 0, 0\n C2 : 1.55, 0, 0\n C3 : 2.04812, 1.44664, 0\n C4 : 1.50806, 2.11919, -1.26369\n O4 : 1.94666, 3.46908, -1.30661\n C5 : -0.0200415, 2.06186, -1.21358\n O5 : -0.475077, 0.686176, -1.1593\n VO5: -0.492509, 0.676579, -1.17187 (virtual)\n VC1: 0.031762, 0.00822503, 0.00564973 (virtual)\n O1 : -0.494034, 0.697555, 1.2082\n O2 : 2.02401, -0.669275, 1.15922\n O3 : 3.4779, 1.4716, 1.64563e-16\n C6 : -0.614146, 2.71298, -2.43962\n O6 : -0.225074, 4.07556, -2.53127\n H1 : -0.370662, -1.03564, 0.00767336\n H2 : 1.90812, -0.520035, -0.900727\n H3 : 1.67301, 1.95456, 0.900727\n H4 : 1.88381, 1.57916, -2.14527\n HO4: 1.61609, 3.94572, -0.516717\n H5 : -0.369153, 2.59396, -0.316372\n HO1: -0.167832, 1.62167, 1.20877\n HO2: 3.00401, -0.669275, 1.15922\n HO3: 3.78886, 2.40096, 5.03844e-17\n 1H6 : -1.71106, 2.65811, -2.3783\n 2H6 : -0.261365, 2.17983, -3.33478\n HO6: -0.621924, 4.47587, -3.33293\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 1: ->4)-alpha-D-Galp:reducing_end:non-reducing_end (Gal, Z):\nBase: ->4)-alpha-D-Galp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: galactose\n IUPAC Name: alpha-D-galactopyranose\n Abbreviation: alpha-D-Galp\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n none\n Polymeric Information:\n Reducing?: yes\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : axial\n O2 : equatorial\n O3 : equatorial\n O4 : axial\n C6 : equatorial\nAtom Coordinates:\n C1 : 0, 0, 0\n C2 : 1.55, 0, 0\n C3 : 2.04812, 1.44664, 0\n C4 : 1.50806, 2.11919, -1.26369\n O4 : 1.98701, 1.42994, -2.4091\n C5 : -0.0200415, 2.06186, -1.21358\n O5 : -0.475077, 0.686176, -1.1593\n VO5: -0.492509, 0.676579, -1.17187 (virtual)\n VC1: 0.031762, 0.00822503, 0.00564973 (virtual)\n O1 : -0.494034, 0.697555, 1.2082\n O2 : 2.02401, -0.669275, 1.15922\n O3 : 3.4779, 1.4716, 1.64563e-16\n C6 : -0.614146, 2.71298, -2.43962\n O6 : -0.225074, 4.07556, -2.53127\n H1 : -0.370662, -1.03564, 0.00767336\n H2 : 1.90812, -0.520035, -0.900727\n H3 : 1.67301, 1.95456, 0.900727\n H4 : 1.85245, 3.16359, -1.28863\n HO4: 2.96665, 1.45445, -2.41977\n H5 : -0.369153, 2.59396, -0.316372\n HO1: -0.167832, 1.62167, 1.20877\n HO2: 3.00401, -0.669275, 1.15922\n HO3: 3.78886, 2.40096, 5.03844e-17\n 1H6 : -1.71106, 2.65811, -2.3783\n 2H6 : -0.261365, 2.17983, -3.33478\n HO6: -0.621924, 4.47587, -3.33293\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 1: ->3)-alpha-D-Manp:reducing_end:non-reducing_end (Man, Z):\nBase: ->3)-alpha-D-Manp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 O3 \n Backbone atoms: C1 C2 C3 O3 C4 C5 O5 VO5 VC1 H1 H2 H3 HO3 H4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O4 C6 O6 HO1 HO2 HO4 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: mannose\n IUPAC Name: alpha-D-mannopyranose\n Abbreviation: alpha-D-Manp\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n none\n Polymeric Information:\n Reducing?: yes\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : axial\n O2 : axial\n O3 : equatorial\n O4 : equatorial\n C6 : equatorial\nAtom Coordinates:\n C1 : 0, 0, 0\n C2 : 1.55, 0, 0\n C3 : 2.04812, 1.44664, 0\n O3 : 3.4779, 1.4716, 1.64563e-16\n C4 : 1.50806, 2.11919, -1.26369\n C5 : -0.0200415, 2.06186, -1.21358\n O5 : -0.475077, 0.686176, -1.1593\n VO5: -0.492509, 0.676579, -1.17187 (virtual)\n VC1: 0.031762, 0.00822503, 0.00564973 (virtual)\n O1 : -0.494034, 0.697555, 1.2082\n O2 : 2.02401, -0.669275, -1.15922\n O4 : 1.94666, 3.46908, -1.30661\n C6 : -0.614146, 2.71298, -2.43962\n O6 : -0.225074, 4.07556, -2.53127\n H1 : -0.370662, -1.03564, 0.00767336\n H2 : 1.90812, -0.520035, 0.900727\n H3 : 1.67301, 1.95456, 0.900727\n HO3: 3.78886, 2.40096, 5.03844e-17\n H4 : 1.88381, 1.57916, -2.14527\n H5 : -0.369153, 2.59396, -0.316372\n HO1: -0.167832, 1.62167, 1.20877\n HO2: 3.00401, -0.669275, -1.15922\n HO4: 1.61609, 3.94572, -0.516717\n 1H6 : -1.71106, 2.65811, -2.3783\n 2H6 : -0.261365, 2.17983, -3.33478\n HO6: -0.621924, 4.47587, -3.33293\nMirrored relative to coordinates in ResidueType: FALSE\n\n59.99999999999999\n-59.99999999999999\n60.00000000000001\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: ../test/data/carbohydrates/Lex.pdb\nTotal residues: 3\nSequence: ZZZ\nFold tree:\nFOLD_TREE EDGE 1 2 -1 EDGE 1 3 -2 O3 C1 \nbeta-D-Galp-(1->4)-beta-D-GlcpNAc\nalpha-L-Fucp-\n.PoseFromSFRBuilder: [ WARNING ] Gal2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Fuc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 3 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/N-linked_14-mer_glycan.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc6 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc7 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man8 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man9 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man10 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man11 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc12 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc13 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc14 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man15 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man16 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man17 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man18 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man19 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 6 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ]Residue 1: ->4)-beta-D-Glcp:reducing_end:->3)-branch:2-AcNH (Glc, Z):\nBase: ->4)-beta-D-Glcp\n Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS BRANCH_POINT POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR C2_MODIFIED ACETYLAMINO_SUGAR\n Variant types: LOWER_TERMINUS_VARIANT C3_BRANCH_POINT C2_ACETYLAMINO_SUGAR\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO4 HO3 HO2 N2 CN2 CAN2 OCN2 HO1 1H6 2H6 HO6 HN2 1HC2 2HC2 3HC2\n Branch-point atoms: O3 \nCarbohydrate Properties for this Residue:\n Basic Name: glucosamine\n IUPAC Name: ->4)-beta-2-(N-acetylamino)-2-deoxy-D-glucopyranose\n Abbreviation: ->4)-beta-D-GlcpNAc\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: beta\n Modifications: \n acetylamino sugar\n Polymeric Information:\n Reducing?: yes\n Main chain connection: (_->4)\n Branch connections: (_->3)\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O1 : equatorial\n N2 : equatorial\n O3 : equatorial\n O4 : equatorial\n C6 : equatorial\nAtom Coordinates:\n C1 : 35.71, 122.693, 36.907\n C2 : 36.264, 121.664, 35.887\n C3 : 35.396, 120.362, 35.896\n C4 : 35.215, 119.833, 37.36\n O4 : 34.235, 118.792, 37.37\n C5 : 34.756, 121.002, 38.316\n O5 : 35.66, 122.104, 38.21\n VO5: 35.66, 122.104, 38.21 (virtual)\n VC1: 35.7109, 122.617, 36.8656 (virtual)\n O1 : 36.369, 123.964, 36.94\n O2 : 36.2371, 122.227, 34.5836 (virtual)\n O3 : 36.026, 119.359, 35.094\n C6 : 34.689, 120.7, 39.82\n O6 : 35.928, 120.224, 40.287\n HO4: 34.615, 117.665, 38.155 (virtual)\n HO3: 35.546, 119.238, 33.75 (virtual)\n HO2: 36.5871, 121.577, 33.9392 (virtual)\n N2 : 36.245, 122.328, 34.583\n CN2: 37.363, 122.3, 33.878\n CAN2: 37.043, 123.112, 32.473\n OCN2: 38.517, 122.472, 34.271\n H1 : 34.6514, 122.845, 36.6496\n H2 : 37.299, 121.411, 36.1601\n H3 : 34.408, 120.587, 35.4681\n H4 : 36.1743, 119.429, 37.7162\n H5 : 33.7421, 121.32, 38.0316\n HO1: 36.301, 124.391, 36.0604\n 1H6 : 33.9192, 119.935, 39.9976\n 2H6 : 34.4315, 121.623, 40.3596\n HO6: 35.8659, 120.037, 41.247\n HN2: 35.4316, 122.782, 34.2477\n 1HC2: 36.3241, 123.919, 32.671\n 2HC2: 36.5729, 122.428, 31.7525\n 3HC2: 37.9836, 123.478, 32.0377\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 2: ->4)-beta-D-Galp:non-reducing_end (Gal, Z):\nBase: ->4)-beta-D-Galp\n Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6\nCarbohydrate Properties for this Residue:\n Basic Name: galactose\n IUPAC Name: beta-D-galactopyranosyl\n Abbreviation: beta-D-Galp-\n Classification: aldohexose\n Stereochemistry: D\n Ring Form: pyranose\n Anomeric Form: beta\n Modifications: \n none\n Polymeric Information:\n Reducing?: no\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60\n O2 : equatorial\n O3 : equatorial\n O4 : axial\n C6 : equatorial\nAtom Coordinates:\n C1 : 34.615, 117.665, 38.155\n C2 : 33.365, 116.921, 38.692\n C3 : 33.836, 115.668, 39.463\n C4 : 34.765, 114.785, 38.592\n O4 : 33.936, 114.234, 37.591\n C5 : 35.931, 115.629, 38.011\n O5 : 35.406, 116.786, 37.348\n VO5: 35.406, 116.786, 37.348 (virtual)\n VC1: 34.6528, 117.616, 38.2521 (virtual)\n O1 : 34.235, 118.792, 37.37 (virtual)\n O2 : 32.626, 117.74, 39.575\n O3 : 32.706, 114.881, 39.893\n C6 : 36.818, 114.855, 37.032\n O6 : 37.611, 113.891, 37.692\n HO1: 35.215, 119.833, 37.36 (virtual)\n H1 : 35.2209, 118.009, 39.0061\n H2 : 32.7301, 116.628, 37.8427\n H3 : 34.3885, 115.986, 40.3595\n H4 : 35.1785, 113.978, 39.2143\n HO4: 33.2273, 113.702, 38.0094\n H5 : 36.5692, 115.975, 38.8375\n HO2: 31.8431, 117.248, 39.8996\n HO3: 33.0232, 114.092, 40.3795\n 1H6 : 37.4842, 115.562, 36.5164\n 2H6 : 36.1787, 114.34, 36.2998\n HO6: 38.1635, 113.417, 37.0358\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 3: ->4)-alpha-L-Fucp:non-reducing_end (Fuc, Z):\nBase: ->4)-alpha-L-Fucp\n Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE L_SUGAR PYRANOSE ALPHA_SUGAR C6_MODIFIED DEOXY_SUGAR\n Variant types: UPPER_TERMINUS_VARIANT C6_DEOXY_SUGAR\n Main-chain atoms: C1 C2 C3 C4 O4 \n Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 \n Ring atoms: C1 C2 C3 C4 C5 O5 \n Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO6 HO2 HO3 1H6 2H6 3H6 \nCarbohydrate Properties for this Residue:\n Basic Name: fucose\n IUPAC Name: alpha-L-fucopyranosyl\n Abbreviation: alpha-L-Fucp-\n Classification: aldohexose\n Stereochemistry: L\n Ring Form: pyranose\n Anomeric Form: alpha\n Modifications: \n deoxy sugar\n Polymeric Information:\n Reducing?: no\n Main chain connection: N/A\n Branch connections: none\nRing Conformer: 1C4 (chair): C-P parameters (q, phi, theta): 0.55, 180, 180; nu angles (degrees): -60, 60, -60, 60, -60, 60\n O2 : equatorial\n O3 : equatorial\n O4 : axial\n C6 : equatorial\nAtom Coordinates:\n C1 : 35.546, 119.238, 33.75\n C2 : 36.615, 118.464, 32.939\n C3 : 36.681, 116.991, 33.421\n C4 : 35.284, 116.331, 33.366\n O4 : 34.915, 116.247, 31.999\n C5 : 34.24, 117.183, 34.142\n O5 : 34.28, 118.546, 33.673\n VO5: 34.28, 118.546, 33.673 (virtual)\n VC1: 35.5799, 119.134, 33.8691 (virtual)\n O1 : 36.026, 119.359, 35.094 (virtual)\n O2 : 37.839, 119.137, 33.073\n O3 : 37.527, 116.202, 32.617\n C6 : 32.809, 116.64, 34.044\n O6 : 32.372, 116.598, 32.6936 (virtual)\n HO1: 35.396, 120.362, 35.896 (virtual)\n HO6: 31.4572, 116.249, 32.6565 (virtual)\n H1 : 35.3955, 120.244, 33.3315\n H2 : 36.3437, 118.489, 31.8733\n H3 : 37.0471, 116.97, 34.4581\n H4 : 35.3419, 115.332, 33.8218\n HO4: 34.8869, 117.147, 31.6118\n H5 : 34.5158, 117.205, 35.2067\n HO2: 38.5305, 118.662, 32.5661\n HO3: 37.538, 115.283, 32.9572\n 1H6 : 32.7831, 115.622, 34.4596\n 2H6 : 32.137, 117.296, 34.6166\n 3H6 : 32.5045, 116.622, 32.9871\nMirrored relative to coordinates in ResidueType: FALSE\n\nPDB file name: ../test/data/carbohydrates/N-linked_14-mer_glycan.pdb\nTotal residues: 19\nSequence: ANASAZZZZZZZZZZZZZZ\nFold tree:\nFOLD_TREE EDGE 1 5 -1 EDGE 2 6 -2 ND2 C1 EDGE 6 14 -1 EDGE 8 15 -2 O6 C1 EDGE 15 17 -1 EDGE 15 18 -2 O6 C1 EDGE 18 19 -1 \nANASA\nalpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-beta-D-GlcpNAc-\nalpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-alpha-D-Manp-\nalpha-D-Manp-(1->2)-alpha-D-Manp-\nPDB file name: ../test/data/carbohydrates/O_glycan.pdb\nTotal residues: 4\nSequence: ASAZ\nFold tree:\nFOLD_TREE EDGE 1 3 -1 EDGE 2 4 -2 OG C1 \nASA\nalpha-D-Glcp-\n missing an atom: 15 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 18 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.import_pose.import_pose: File '../test/data/carbohydrates/O_glycan.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc4 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 4 H1 that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->4)-alpha-D-Glcp:non-reducing_end anchor: OG 2 root: C1 \ncore.pose.carbohydrates.util: Glycosylated pose with a(n) Glcp-OGSER2 bond.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose.carbohydrates.util: Idealizing glycosidic torsions.\ncore.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->3)-alpha-D-Galp:2-AcNH anchor: OG 2 root: C1 \ncore.pose.carbohydrates.util: Glycosylated pose with a(n) a-D-GalpNAc-(1->3)-a-D-GalpNAc--OGSER2 bond.\ncore.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees\ncore.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees.\ncore.pose.carbohydrates.util: Idealizing glycosidic torsions.\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.core.pose import pose_from_saccharide_sequence\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:42: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for res in lactose: print( res.seqpos(), res.name() )\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:43: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for res in maltotriose: print( res.seqpos(), res.name() )\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:128: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for res in Lex: print( res )\n\nFinished C001_Carbohydrates_Demo01 in 0:00:58.696160", "state": "passed"}, "D010_Pose_structure": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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================================================================================\nLoaded from ../test/data/test_in.pdb\n116 residues\n1 chain(s) ('A')\nSequence:\nDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL\nSecondary Structure:\nLHHHHHHHHHHHHLLLLLLLLLHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHLLLLLLLLLLLLLL\n\t63.7% Helical\n\t0.0% Sheet\n\t36.2% Loop\n================================================================================\nPose numbered Residue 58\nPDB numbered Residue 58\nSingle Letter: T\nChain: A\nSecondary Structure: Helix\nPhi: -66.10647574201566\nPsi: -37.61278973721053\nOmega: 179.87870721715393\nChi 1: 157.77746590432218\nChi 2: 179.99312165369778\n================================================================================\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.39261 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nprotocols.DsspMover: LHHHHHHHHHHHHLLLLLLLLLHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHLLLLHHHHHHHHHHHHLLLHHHHHLLLLLLLLLLLLLL\n\nFinished D010_Pose_structure in 0:00:47.564459", "state": "passed"}, "D020_Pose_scoring": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.48128 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.651765 seconds to load from binary\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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================================================================================\nScoreFunction a: 949.3120641217321\nScoreFunction b: 949.3120641217321\nScoreFunction c: 54.59531500723148\nScoreFunction d: 54.59531500723148\nScoreFunction e: 639.6921382071229\n================================================================================\nLoaded from ../test/data/test_in.pdb\n116 residues\nRadius of Gyration ~ 15.070968422880075\nTotal Rosetta Score: 639.6921382071229\n================================================================================\nPose numbered Residue 58\nTotal Residue Score: 17.835676002501447\nScore Breakdown:\n---------------------------------------------\n\tfa_atr :\t -6.767255537709819\n\tfa_rep :\t 18.770496833063742\n\tfa_sol :\t 4.234940603509646\n\tfa_intra_rep :\t 0.0152272562193792\n\tfa_elec :\t -1.0892415802359439\n\tpro_close :\t 0.0\n\thbond_sr_bb :\t 0.0\n\thbond_lr_bb :\t 0.0\n\thbond_bb_sc :\t 0.0\n\thbond_sc :\t 0.0\n\tdslf_fa13 :\t 0.0\n\trama :\t -0.1350781930896833\n\tomega :\t -0.006962209630292475\n\tfa_dun :\t 3.0402048792529595\n\tp_aa_pp :\t 0.043343951121461756\n\tref :\t -0.27\n---------------------------------------------\nHydrogen bonds involving Residue 58:\n58 H => 54 O |score: -0.9409534230157675\n62 H => 58 O |score: -0.7406209609222881\n================================================================================\n Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.800 -715.300 -572.240\n fa_rep 0.440 827.739 364.205\n fa_sol 0.750 504.855 378.642\n fa_intra_rep 0.004 563.466 2.254\n fa_elec 0.700 -133.742 -93.619\n pro_close 1.000 17.220 17.220\n hbond_sr_bb 1.170 -47.398 -55.455\n hbond_lr_bb 1.170 -0.785 -0.918\n hbond_bb_sc 1.170 -5.673 -6.637\n hbond_sc 1.100 -1.540 -1.693\n dslf_fa13 1.000 0.000 0.000\n rama 0.200 4.872 0.974\n omega 0.500 16.053 8.026\n fa_dun 0.560 1133.922 634.996\n p_aa_pp 0.320 -17.819 -5.702\n ref 1.000 -30.360 -30.360\n---------------------------------------------------\n Total weighted score: 639.692\n\nFinished D020_Pose_scoring in 0:02:36.799735", "state": "passed"}, "D030_Fold_tree": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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\nThe first FoldTree is proper: True\nThe second FoldTree is proper: True\n\nlinearized structure output\npre jump perturbed structure output\nfirst internal jump edge perturbed structure output\nsecond internal jump edge perturbed structure output\npost jump perturbed structure output\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.39312 seconds.\n\nFinished D030_Fold_tree in 0:00:46.164739", "state": "passed"}, "D040_Movemap": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.45335 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n resnum BB CHI NU BRANCH\n 001 TRUE FALSE FALSE FALSE\n 002 TRUE FALSE FALSE FALSE\n 003 TRUE FALSE FALSE FALSE\n 004 TRUE FALSE FALSE FALSE\n 005 TRUE FALSE FALSE FALSE\n 006 TRUE FALSE FALSE FALSE\n 007 TRUE FALSE FALSE FALSE\n 008 TRUE FALSE FALSE FALSE\n 009 TRUE FALSE FALSE FALSE\n 010 TRUE FALSE FALSE FALSE\n 011 TRUE FALSE FALSE FALSE\n 012 TRUE FALSE FALSE FALSE\n 013 TRUE FALSE FALSE FALSE\n 014 TRUE FALSE FALSE FALSE\n 015 TRUE FALSE FALSE FALSE\n 016 TRUE FALSE FALSE FALSE\n 017 TRUE FALSE FALSE FALSE\n 018 TRUE FALSE FALSE FALSE\n 019 TRUE FALSE FALSE FALSE\n 020 TRUE FALSE FALSE FALSE\n 021 TRUE FALSE FALSE FALSE\n 022 TRUE FALSE FALSE FALSE\n 023 TRUE FALSE FALSE FALSE\n 024 TRUE FALSE FALSE FALSE\n 025 TRUE FALSE FALSE FALSE\n 026 TRUE FALSE FALSE FALSE\n 027 TRUE FALSE FALSE FALSE\n 028 TRUE FALSE FALSE FALSE\n 029 TRUE FALSE FALSE FALSE\n 030 TRUE FALSE FALSE FALSE\n 031 TRUE FALSE FALSE FALSE\n 032 TRUE FALSE FALSE FALSE\n 033 TRUE FALSE FALSE FALSE\n 034 TRUE FALSE FALSE FALSE\n 035 TRUE FALSE FALSE FALSE\n 036 TRUE FALSE FALSE FALSE\n 037 TRUE FALSE FALSE FALSE\n 038 TRUE FALSE FALSE FALSE\n 039 TRUE FALSE FALSE FALSE\n 040 TRUE FALSE FALSE FALSE\n 041 TRUE FALSE FALSE FALSE\n 042 TRUE FALSE FALSE FALSE\n 043 TRUE FALSE FALSE FALSE\n 044 TRUE FALSE FALSE FALSE\n 045 TRUE FALSE FALSE FALSE\n 046 TRUE FALSE FALSE FALSE\n 047 TRUE FALSE FALSE FALSE\n 048 TRUE FALSE FALSE FALSE\n 049 TRUE FALSE FALSE FALSE\n 050 TRUE FALSE FALSE FALSE\n 051 TRUE FALSE FALSE FALSE\n 052 TRUE FALSE FALSE FALSE\n 053 TRUE FALSE FALSE FALSE\n 054 TRUE FALSE FALSE FALSE\n 055 TRUE FALSE FALSE FALSE\n 056 TRUE FALSE FALSE FALSE\n 057 TRUE FALSE FALSE FALSE\n 058 TRUE FALSE FALSE FALSE\n 059 TRUE FALSE FALSE FALSE\n 060 TRUE FALSE FALSE FALSE\n 061 TRUE FALSE FALSE FALSE\n 062 TRUE FALSE FALSE FALSE\n 063 TRUE FALSE FALSE FALSE\n 064 TRUE FALSE FALSE FALSE\n 065 TRUE FALSE FALSE FALSE\n 066 TRUE FALSE FALSE FALSE\n 067 TRUE FALSE FALSE FALSE\n 068 TRUE FALSE FALSE FALSE\n 069 TRUE FALSE FALSE FALSE\n 070 TRUE FALSE FALSE FALSE\n 071 TRUE FALSE FALSE FALSE\n 072 TRUE FALSE FALSE FALSE\n 073 TRUE FALSE FALSE FALSE\n 074 TRUE FALSE FALSE FALSE\n 075 TRUE FALSE FALSE FALSE\n 076 TRUE FALSE FALSE FALSE\n 077 TRUE FALSE FALSE FALSE\n 078 TRUE FALSE FALSE FALSE\n 079 TRUE FALSE FALSE FALSE\n 080 TRUE FALSE FALSE FALSE\n 081 TRUE FALSE FALSE FALSE\n 082 TRUE FALSE FALSE FALSE\n 083 TRUE FALSE FALSE FALSE\n 084 TRUE FALSE FALSE FALSE\n 085 TRUE FALSE FALSE FALSE\n 086 TRUE FALSE FALSE FALSE\n 087 TRUE FALSE FALSE FALSE\n 088 TRUE FALSE FALSE FALSE\n 089 TRUE FALSE FALSE FALSE\n 090 TRUE FALSE FALSE FALSE\n 091 TRUE FALSE FALSE FALSE\n 092 TRUE FALSE FALSE FALSE\n 093 TRUE FALSE FALSE FALSE\n 094 TRUE FALSE FALSE FALSE\n 095 TRUE FALSE FALSE FALSE\n 096 TRUE FALSE FALSE FALSE\n 097 TRUE FALSE FALSE FALSE\n 098 TRUE FALSE FALSE FALSE\n 099 TRUE FALSE FALSE FALSE\n 100 TRUE FALSE FALSE FALSE\n 101 TRUE FALSE FALSE FALSE\n 102 TRUE FALSE FALSE FALSE\n 103 TRUE FALSE FALSE FALSE\n 104 TRUE FALSE FALSE FALSE\n 105 TRUE FALSE FALSE FALSE\n 106 TRUE FALSE FALSE FALSE\n 107 TRUE FALSE FALSE FALSE\n 108 TRUE FALSE FALSE FALSE\n 109 TRUE FALSE FALSE FALSE\n 110 TRUE FALSE FALSE FALSE\n 111 TRUE FALSE FALSE FALSE\n 112 TRUE FALSE FALSE FALSE\n 113 TRUE FALSE FALSE FALSE\n 114 TRUE FALSE FALSE FALSE\n 115 TRUE FALSE FALSE FALSE\n 116 TRUE FALSE FALSE FALSE\nPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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\nPre minimization score: 949.3120641217321\nPost minimization score: 676.3237392681959\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/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.659815 seconds to load from binary\n\nFinished D040_Movemap in 0:02:57.302737", "state": "passed"}, "D050_Packer_task": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.46518 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.684901 seconds to load from binary\ncore.pack.pack_rotamers: built 3014 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1684 PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tASP:NtermProteinFull\n2\tTRUE\tFALSE\tALA\n3\tTRUE\tFALSE\tILE\n4\tTRUE\tFALSE\tTHR\n5\tTRUE\tFALSE\tILE\n6\tTRUE\tFALSE\tHIS,HIS_D\n7\tTRUE\tFALSE\tSER\n8\tTRUE\tFALSE\tILE\n9\tTRUE\tFALSE\tLEU\n10\tTRUE\tFALSE\tASP\n11\tTRUE\tFALSE\tTRP\n12\tTRUE\tFALSE\tILE\n13\tTRUE\tFALSE\tGLU\n14\tTRUE\tFALSE\tASP\n15\tTRUE\tFALSE\tASN\n16\tTRUE\tFALSE\tLEU\n17\tTRUE\tFALSE\tGLU\n18\tTRUE\tFALSE\tSER\n19\tTRUE\tFALSE\tPRO\n20\tTRUE\tFALSE\tLEU\n21\tTRUE\tFALSE\tSER\n22\tTRUE\tFALSE\tLEU\n23\tTRUE\tFALSE\tGLU\n24\tTRUE\tFALSE\tLYS\n25\tTRUE\tFALSE\tVAL\n26\tTRUE\tFALSE\tSER\n27\tTRUE\tFALSE\tGLU\n28\tTRUE\tFALSE\tARG\n29\tTRUE\tFALSE\tSER\n30\tTRUE\tFALSE\tGLY\n31\tTRUE\tFALSE\tTYR\n32\tTRUE\tFALSE\tSER\n33\tTRUE\tFALSE\tLYS\n34\tTRUE\tFALSE\tTRP\n35\tTRUE\tFALSE\tHIS,HIS_D\n36\tTRUE\tFALSE\tLEU\n37\tTRUE\tFALSE\tGLN\n38\tTRUE\tFALSE\tARG\n39\tTRUE\tFALSE\tMET\n40\tTRUE\tFALSE\tPHE\n41\tTRUE\tFALSE\tLYS\n42\tTRUE\tFALSE\tLYS\n43\tTRUE\tFALSE\tGLU\n44\tTRUE\tFALSE\tTHR\n45\tTRUE\tFALSE\tGLY\n46\tTRUE\tFALSE\tHIS,HIS_D\n47\tTRUE\tFALSE\tSER\n48\tTRUE\tFALSE\tLEU\n49\tTRUE\tFALSE\tGLY\n50\tTRUE\tFALSE\tGLN\n51\tTRUE\tFALSE\tTYR\n52\tTRUE\tFALSE\tILE\n53\tTRUE\tFALSE\tARG\n54\tTRUE\tFALSE\tSER\n55\tTRUE\tFALSE\tARG\n56\tTRUE\tFALSE\tLYS\n57\tTRUE\tFALSE\tMET\n58\tTRUE\tFALSE\tTHR\n59\tTRUE\tFALSE\tGLU\n60\tTRUE\tFALSE\tILE\n61\tTRUE\tFALSE\tALA\n62\tTRUE\tFALSE\tGLN\n63\tTRUE\tFALSE\tLYS\n64\tTRUE\tFALSE\tLEU\n65\tTRUE\tFALSE\tLYS\n66\tTRUE\tFALSE\tGLU\n67\tTRUE\tFALSE\tSER\n68\tTRUE\tFALSE\tASN\n69\tTRUE\tFALSE\tGLU\n70\tTRUE\tFALSE\tPRO\n71\tTRUE\tFALSE\tILE\n72\tTRUE\tFALSE\tLEU\n73\tTRUE\tFALSE\tTYR\n74\tTRUE\tFALSE\tLEU\n75\tTRUE\tFALSE\tALA\n76\tTRUE\tFALSE\tGLU\n77\tTRUE\tFALSE\tARG\n78\tTRUE\tFALSE\tTYR\n79\tTRUE\tFALSE\tGLY\n80\tTRUE\tFALSE\tPHE\n81\tTRUE\tFALSE\tGLU\n82\tTRUE\tFALSE\tSER\n83\tTRUE\tFALSE\tGLN\n84\tTRUE\tFALSE\tGLN\n85\tTRUE\tFALSE\tTHR\n86\tTRUE\tFALSE\tLEU\n87\tTRUE\tFALSE\tTHR\n88\tTRUE\tFALSE\tARG\n89\tTRUE\tFALSE\tTHR\n90\tTRUE\tFALSE\tPHE\n91\tTRUE\tFALSE\tLYS\n92\tTRUE\tFALSE\tASN\n93\tTRUE\tFALSE\tTYR\n94\tTRUE\tFALSE\tPHE\n95\tTRUE\tFALSE\tASP\n96\tTRUE\tFALSE\tVAL\n97\tTRUE\tFALSE\tPRO\n98\tTRUE\tFALSE\tPRO\n99\tTRUE\tFALSE\tHIS,HIS_D\n100\tTRUE\tFALSE\tLYS\n101\tTRUE\tFALSE\tTYR\n102\tTRUE\tFALSE\tARG\n103\tTRUE\tFALSE\tMET\n104\tTRUE\tFALSE\tTHR\n105\tTRUE\tFALSE\tASN\n106\tTRUE\tFALSE\tMET\n107\tTRUE\tFALSE\tGLN\n108\tTRUE\tFALSE\tGLY\n109\tTRUE\tFALSE\tGLU\n110\tTRUE\tFALSE\tSER\n111\tTRUE\tFALSE\tARG\n112\tTRUE\tFALSE\tPHE\n113\tTRUE\tFALSE\tLEU\n114\tTRUE\tFALSE\tHIS,HIS_D\n115\tTRUE\tFALSE\tPRO\n116\tTRUE\tFALSE\tLEU:CtermProteinFull\n\n\nPre packing score: 949.3120641217321\nPost packing score: 119.97075192656075\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tFALSE\tFALSE\t\n2\tFALSE\tFALSE\t\n3\tFALSE\tFALSE\t\n4\tFALSE\tFALSE\t\n5\tFALSE\tFALSE\t\n6\tFALSE\tFALSE\t\n7\tFALSE\tFALSE\t\n8\tFALSE\tFALSE\t\n9\tFALSE\tFALSE\t\n10\tFALSE\tFALSE\t\n11\tFALSE\tFALSE\t\n12\tFALSE\tFALSE\t\n13\tFALSE\tFALSE\t\n14\tFALSE\tFALSE\t\n15\tFALSE\tFALSE\t\n16\tFALSE\tFALSE\t\n17\tFALSE\tFALSE\t\n18\tFALSE\tFALSE\t\n19\tFALSE\tFALSE\t\n20\tFALSE\tFALSE\t\n21\tFALSE\tFALSE\t\n22\tFALSE\tFALSE\t\n23\tFALSE\tFALSE\t\n24\tFALSE\tFALSE\t\n25\tFALSE\tFALSE\t\n26\tFALSE\tFALSE\t\n27\tFALSE\tFALSE\t\n28\tFALSE\tFALSE\t\n29\tFALSE\tFALSE\t\n30\tFALSE\tFALSE\t\n31\tFALSE\tFALSE\t\n32\tFALSE\tFALSE\t\n33\tFALSE\tFALSE\t\n34\tFALSE\tFALSE\t\n35\tFALSE\tFALSE\t\n36\tFALSE\tFALSE\t\n37\tFALSE\tFALSE\t\n38\tFALSE\tFALSE\t\n39\tFALSE\tFALSE\t\n40\tFALSE\tFALSE\t\n41\tFALSE\tFALSE\t\n42\tFALSE\tFALSE\t\n43\tFALSE\tFALSE\t\n44\tFALSE\tFALSE\t\n45\tFALSE\tFALSE\t\n46\tFALSE\tFALSE\t\n47\tFALSE\tFALSE\t\n48\tFALSE\tFALSE\t\n49\tFALSE\tFALSE\t\n50\tFALSE\tFALSE\t\n51\tFALSE\tFALSE\t\n52\tFALSE\tFALSE\t\n53\tFALSE\tFALSE\t\n54\tFALSE\tFALSE\t\n55\tFALSE\tFALSE\t\n56\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n57\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n58\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n59\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n60\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n61\tFALSE\tFALSE\t\n62\tFALSE\tFALSE\t\n63\tFALSE\tFALSE\t\n64\tFALSE\tFALSE\t\n65\tFALSE\tFALSE\t\n66\tFALSE\tFALSE\t\n67\tFALSE\tFALSE\t\n68\tFALSE\tFALSE\t\n69\tFALSE\tFALSE\t\n70\tFALSE\tFALSE\t\n71\tFALSE\tFALSE\t\n72\tFALSE\tFALSE\t\n73\tFALSE\tFALSE\t\n74\tFALSE\tFALSE\t\n75\tFALSE\tFALSE\t\n76\tFALSE\tFALSE\t\n77\tFALSE\tFALSE\t\n78\tFALSE\tFALSE\t\n79\tFALSE\tFALSE\t\n80\tFALSE\tFALSE\t\n81\tFALSE\tFALSE\t\n82\tFALSE\tFALSE\t\n83\tFALSE\tFALSE\t\n84\tFALSE\tFALSE\t\n85\tFALSE\tFALSE\t\n86\tFALSE\tFALSE\t\n87\tFALSE\tFALSE\t\n88\tFALSE\tFALSE\t\n89\tFALSE\tFALSE\t\n90\tFALSE\tFALSE\t\n91\tFALSE\tFALSE\t\n92\tFALSE\tFALSE\t\n93\tFALSE\tFALSE\t\n94\tFALSE\tFALSE\t\n95\tFALSE\tFALSE\t\n96\tFALSE\tFALSE\t\n97\tFALSE\tFALSE\t\n98\tFALSE\tFALSE\t\n99\tFALSE\tFALSE\t\n100\tFALSE\tFALSE\t\n101\tFALSE\tFALSE\t\n102\tFALSE\tFALSE\t\n103\tFALSE\tFALSE\t\n104\tFALSE\tFALSE\t\n105\tFALSE\tFALSE\t\n106\tFALSE\tFALSE\t\n107\tFALSE\tFALSE\t\n108\tFALSE\tFALSE\t\n109\tFALSE\tFALSE\t\n110\tFALSE\tFALSE\t\n111\tFALSE\tFALSE\t\n112\tFALSE\tFALSE\t\n113\tFALSE\tFALSE\t\n114\tFALSE\tFALSE\t\n115\tFALSE\tFALSE\t\n116\tFALSE\tFALSE\t\n\n\nDesign with all proteogenic amino acids at (pose numbered) residues 56 to 60\nPre-design score: 949.3120641217321\nPre-design sequence: ...SRKMTEIAQ...\n\nPost-design score: 880.7910264455669\nPost-design sequence: ...SRIATEIAQ...\nrotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\n\nFinished D050_Packer_task in 0:05:49.468866", "state": "passed"}, "D060_Folding": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.39335 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.159927 seconds.\ncore.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibraryPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nWorking on decoy: fold_output_0.pdb\n================================================================================\nPotential Disulfides:\n================================================================================\n===== Centroid Scores =====\nOriginal Score\t:\t 445.279574904899\nfold_output_1 \t:\t 131.88750967869055\n: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.72417 seconds to load from binary\n\nFinished D060_Folding in 0:02:39.159236", "state": "passed"}, "D070_Refinement": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.36544 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.672166 seconds to load from binary\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.pack_rotamers: built 2998 rotamerKilled\n\nFinished D070_Refinement in 0:17:04.205205", "state": "failed"}, "D080_Loop_modeling": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -run:jran 1111125 -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111125 seed_offset=0 real_seed=1111125\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111125 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.43729 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nprotocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 14 -1 EDGE 14 17 -1 EDGE 14 20 1 EDGE 20 18 -1 EDGE 20 116 -1 \nprotocols.loops.loops_main: Added cutpoint variant to residue 17\nprotocols.loops.loops_main: Added cutpoint variant to residue 18\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.151936 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.6718 seconds to load from binary\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.pack_rotamers: built 1795 rotamers at 116 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loops_main: Added cutpoint variant to residue 17\nprotocols.loops.loops_main: Added cutpoint variant to residue 18\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 825 rotamers at 28 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 138.566 138.566\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 1 138.566\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 74.5737 74.5737\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 70.5721 70.5721\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.7173 62.7173\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.0971 61.0971\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 59.9547 59.9547\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 60.9978 59.9547\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.0257 59.9547\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.1107 59.9547\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.8625 59.9547\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 58.3835 58.3835\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.056 55.056\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.056 55.056\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.067 55.056\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.067 55.056\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.044 55.044\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 55.044 55.044\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9313 54.9313\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.9875 54.9313\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.8935 54.8935\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.8935 54.8935\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 782 rotamers at 25 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 54.3482 54.3482\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 2 62.8306\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.5788 62.5788\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 62.4828 62.4828\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 65.0013 62.4828\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9031 62.4828\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 61.7638 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9001 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9169 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9632 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.9015 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8807 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 64.8807 61.7638\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_sco/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/demo/D080_Loop_modeling.py:131: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.loops.loop_mover.refine import LoopMover_Refine_CCD\nKilled\n\nFinished D080_Loop_modeling in 0:17:04.167815", "state": "failed"}, "D090_Ala_scan": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.43269 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: current variant for 1 CYS\ncore.conformation.Conformation: current variant for 119 CYS\ncore.conformation.Conformation: current variant for 1 CYD\ncore.conformation.Conformation: current variant for 119 CYD\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 56 CYS\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: current variant for 56 CYD\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: current variant for 133 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 133 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: current variant for 161 CYS\ncore.conformation.Conformation: current variant for 175 CYS\ncore.conformation.Conformation: current variant for 161 CYD\ncore.conformation.Conformation: current variant for 175 CYD\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.conformation.Conformation: current variant for 184 CYS\ncore.conformation.Conformation: current variant for 213 CYS\ncore.conformation.Conformation: current variant for 184 CYD\ncore.conformation.Conformation: current variant for 213 CYD\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.712859 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 180 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 189 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 176 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 185 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 463 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 481 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 374 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 392 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 253 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 288 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 222 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 244 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 0 rotamers at 0 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 382 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 403 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 382 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 403 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 761 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 769 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 761 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 769 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 661 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 701 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 583 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 623 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 0 rotamers at 0 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 479 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 487 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 479 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 487 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 450 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 477 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 442 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 469 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 400 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 422 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 494 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 516 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 193 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 217 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 165 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 189 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 115 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 123 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 62 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 70 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 184 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 185 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 160 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 160 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 152 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 175 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 86 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 109 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 694 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 694 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 378 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 378 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 0 rotamers at 0 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.thread_manager.RosettaThreadManager: [ WARNING ] A work vector of size zero was passed to the RosettaThreadManager! Duly returning without doing anything.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 451 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 476 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 451 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 476 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 271 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 306 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 241 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 262 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 334 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 369 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 388 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 423 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 573 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 598 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 543 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 560 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 837 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 877 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 676 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 716 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 675 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 688 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 453 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 466 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 747 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 747 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 745 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 745 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 643 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 675 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 482 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 514 rotamers at 18 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 551 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 578 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 514 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 513 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 860 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 916 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 866 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 868 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 819 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 819 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 658 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 658 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 512 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 620 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 405 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 513 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 491 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 491 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 438 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 438 rotamers at 6 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 457 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 485 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 454 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 482 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 377 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 377 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 373 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 373 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 349 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 295 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 331 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 277 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 430 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 538 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 168 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 276 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 217 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 325 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 164 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 164 rotamers at 9 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 509 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 638 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 490 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 600 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 289 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 453 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 287 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 451 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 523 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 563 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 416 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 456 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 629 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 723 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 634 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 733 rotamers at 15 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 460 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 492 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 426 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 450 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 420 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 468 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 414 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 454 rotamers at 13 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 179 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 212 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 82 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 113 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 136 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 148 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 127 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 139 rotamers at 8 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 285 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 285 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 194 rotamers at 12 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 194 rotamers at 12 positions.\ncore.pack.interaction_graph.interacPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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================================================================================\nTrial 1\nMutants (PDB numbered)\t\"ddG\" (interaction dependent score change)\nF39A\t0.3037419927816529\nH40A\t0.06229129148559309\nF41A\t-0.5179182491852998\nC42A\t0.0\nA55A\t0.7526408562292772\nH57A\t-1.8773173484215704\nC58A\t-0.21937284583896144\nI99A\t0.8234264858266727\nG142A\t0.010933632634589685\nL143A\t1.3741232149201892\nT151A\t0.4383926294235607\nW172A\t1.090970767531445\nK175A\t-0.17668088813616123\nS190A\t-0.43304128739850967\nC191A\t0.0\nM192A\t-0.3059494545528878\nG193A\t-1.0066840572941373\nD194A\t0.7375507270811568\nS195A\t-3.072403605791095\nG196A\t-0.6563573918885481\nV213A\t0.558657371203708\nS214A\t-1.1522661010585864\nW215A\t-1.1097669426314951\nG216A\t-1.4328724668492043\nS217A\t-0.3300597192743453\nS218A\t-3.1289141356608923\nT219A\t-0.15885643344037703\nV227A\t-0.14919286886234318\nL37A\t-0.07817160632208697\nE39A\t-0.2842576324672734\nG40A\t-0.351762054102835\nS41A\t-0.3295442811996736\nP42A\t1.3097229786823732\nV43A\t1.5310898302001306\nT44A\t-1.7214007763348604\nL45A\t0.8101922525754901\nD46A\t-4.459550972224804\nL47A\t0.755605431254935\nR48A\t-0.5921687568394418\nY49A\t-1.1555400302183898\nR53A\t-0.022780401792829252\nF55A\t-1.3537481969088958\nG70A\t0.04813369810437962\n================================================================================\nLikely Hotspot Residues\nH57A\nL143A\nW172A\nS195A\nS218A\nP42A\nV43A\nT44A\nD46A\n================================================================================\ntion_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 407 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 353 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 372 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 318 rotamers at 14 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 170 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 210 rotamers at 10 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 188 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 228 rotamers at 11 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/demo/D090_Ala_scan.py:84: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.scoring import Interface\n\nFinished D090_Ala_scan in 0:14:19.373102", "state": "passed"}, "D100_Docking": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.47729 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: current variant for 1 CYS\ncore.conformation.Conformation: current variant for 119 CYS\ncore.conformation.Conformation: current variant for 1 CYD\ncore.conformation.Conformation: current variant for 119 CYD\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 56 CYS\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: current variant for 56 CYD\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: current variant for 133 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 133 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: current variant for 161 CYS\ncore.conformation.Conformation: current variant for 175 CYS\ncore.conformation.Conformation: current variant for 161 CYD\ncore.conformation.Conformation: current variant for 175 CYD\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.conformation.Conformation: current variant for 184 CYS\ncore.conformation.Conformation: current variant for 213 CYS\ncore.conformation.Conformation: current variant for 184 CYD\ncore.conformation.Conformation: current variant for 213 CYD\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.676806 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.192024 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.docking.DockingInitialPerturbation: Reading options...\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.moves.RigidBodyMover: Randomize: Jump (before): RT -0.43256 0.815075 -0.385415 -0.869462 -0.490229 -0.0609182 -0.238594 0.308753 0.92073 -20.1643 -14.8001 1.00855 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (before): 7.27132 -0.353633 18.2062\nprotocols.geometry.RB_geometry: random_reorientation_matrix phi: 99.6306 psi: 274.195 theta: 88.635\nprotocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.501566 0.0943906 -0.859955 -0.450893 -0.819823 -0.352967 -0.738328 0.564784 -0.368635 1.19304 -6.08076 -26.9467 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (after): 7.27132 -0.353633 18.2062\nprotocols.moves.RigidBodyMover: Randomize: ---\nprotocols.moves.RigidBodyMover: Randomize: Jump (before): RT 0.501566 0.0943906 -0.859955 -0.450893 -0.819823 -0.352967 -0.738328 0.564784 -0.368635 1.19304 -6.08076 -26.9467 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (before): 14.3539 25.5364 12.8647\nprotocols.geometry.RB_geometry: random_reorientation_matrix phi: 168.165 psi: 253.962 theta: 126.406\nprotocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.90194 0.265425 -0.340666 0.355013 -0.00652657 0.934839 0.245906 -0.964109 -0.100116 3.28027 -14.8952 32.2801 \nprotocols.moves.RigidBodyMover: Randomize: Rot. Center (after): 26.3065 0.818941 -13.1763\nprotocols.moves.RigidBodyMover: Randomize: ---\nprotocols.moves.RigidBodyMover: Spin: Jump (before): RT 0.904505 0.256377 -0.340796 0.348103 0.017797 0.937287 0.246364 -0.966413 -0.0731481 7.43102 0.0211541 38.4478 \nprotocols.moves.RigidBodyMover: Spin: Rot (before): 15.2576 -9.26054 -20.5784\nprotocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.96652 0.250828 -0.0540836 0.0814818 -0.10016 0.991629 0.243312 -0.962836 -0.117244 6.83388 -0.112006 38.5401 \nprotocols.moves.RigidBodyMover: Spin: Rot (after): 15.2576 -9.26054 -20.5784\nprotocols.moves.RigidBodyMover: Spin: ---\nprotocols.docking.DockingInitialPerturbation: sliding into contact\nprotocols.docking.DockingInitialPerturbation: Moving away\nprotocols.docking.DockingInitialPerturbation: Moving together\nbasic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score\nprotocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!\nprotocols.docking.DockingProtocol: Setting docking foldtree\nprotocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 \nprotocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 \nprotocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingProtocol: /// Rosetta 3 Docking Protocol ///\nprotocols.docking.DockingProtocol: /// ///\nprotocols.docking.DockingProtocol: /// Dockable Jumps: 1 ///\nprotocols.docking.DockingProtocol: /// Low Resolution Docking Protocol: on ///\nprotocols.docking.DockingProtocol: /// High Resolution Docking Protocol: on ///\nprotocols.docking.DockingProtocol: /// Low Resolution Filter: on ///\nprotocols.docking.DockingProtocol: /// High Resolution Filter: on ///\nprotocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingProtocol: FOLD_TREE EDGE 1 190 -1 EDGE 190 238 -1 EDGE 190 285 1 EDGE 285 239 -1 EDGE 285 301 -1 \nprotocols.docking.DockingInitialPerturbation: sliding into contact for centroid mode\nprotocols.docking.DockingInitialPerturbation: sliding into contact\nprotocols.docking.DockingInitialPerturbation: Moving away\nprotocols.docking.DockingInitialPerturbation: Moving together\nprotocols.docking.DockingProtocol: finished initial perturbation\nprotocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... \nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.32\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.1\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.1\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.06\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.14\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.04\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.14\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 4 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 8 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 9 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 10 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 11 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 13 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 14 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 15 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 16 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 19 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 20 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 21 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 22 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 24 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 25 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 26 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 27 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 28 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 29 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 30 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 31 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 32 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 33 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 35 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 37 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 38 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 39 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 40 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 43 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 44 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 45 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 46 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 47 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 48 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 49 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 50 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 51 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 52 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 53 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 54 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 55 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 56 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 58 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 59 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 60 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 61 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 62 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 63 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 64 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 66 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 68 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 69 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 70 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 71 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 73 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 74 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 75 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 77 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 78 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 79 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 80 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 81 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 82 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 83 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 85 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 86 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 87 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 88 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 89 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 91 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 92 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 93 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 94 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 95 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 96 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 97 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 98 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 99 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 100 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 101 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 103 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 104 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 105 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 106 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 107 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 108 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 110 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 112 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 114 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 115 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 116 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 117 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 118 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 119 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 120 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 121 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 122 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 123 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 124 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 125 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 126 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 127 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 128 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 129 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 131 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 132 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 133 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 134 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 135 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 136 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 138 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 141 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 143 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 144 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 145 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 146 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 148 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 149 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 150 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 151 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 152 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 153 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 154 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 155 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 156 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 157 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 158 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 159 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 160 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 161 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 165 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 167 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 168 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 169 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 170 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 171 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 172 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 173 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 174 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 175 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 176 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 178 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 179 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 181 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 182 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 183 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 184 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 185 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 187 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 188 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 191 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 192 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 193 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 194 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 195 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 197 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 199 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 200 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 201 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 202 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 203 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 205 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 206 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 207 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 208 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 210 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 211 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 212 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 213 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 214 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 215 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 216 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 217 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 218 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 221 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 222 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 223 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 224 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 225 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 226 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 227 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 228 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 229 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 230 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 231 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 233 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 234 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 235 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 236 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 237 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 238 because of missing atom number 6 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 240 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 241 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 242 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 243 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 244 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 245 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 248 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 249 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 250 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 251 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 252 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 253 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 254 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 255 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 256 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 257 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 258 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 260 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 261 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 262 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 263 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 264 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 265 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 266 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 267 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 268 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 269 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 270 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 273 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 274 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 275 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 276 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 277 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 278 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 279 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 282 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 283 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 284 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 285 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 287 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 289 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 291 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 292 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 293 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 294 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 295 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 296 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 297 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 298 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 299 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 300 because of missing atom number 5 atom name CB \ncore.pack.pack_rotamers: built 7982 rotamers at 274 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.docking.DockingProtocol: Score before repack:\nprotocols.docking.DockingProtocol: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.338 -1751.322 -591.947\n fa_rep 0.186 8417.226 1562.910\n fa_sol 0.242 975.051 235.962\n fa_elec 0.026 -338.684 -8.806\n fa_pair 0.164 -33.981 -5.573\n hbond_sr_bb 0.245 -47.347 -11.600\n hbond_lr_bb 0.245 -100.043 -24.511\n hbond_bb_sc 0.245 -24.902 -6.101\n hbond_sc 0.245 -6.857 -1.680\n dslf_ss_dst 0.500 -15.294 -7.647\n dslf_cs_ang 2.000 1.100 2.200\n dslf_ss_dih 5.000 0.462 2.308\n dslf_ca_dih 5.000 0.254 1.269\n fa_dun 0.036 1557.509 56.070\n---------------------------------------------------\n Total weighted score: 1202.856\ncore.pack.pack_rotamers: built 4094 rotamers at 291 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.docking.DockingProtocol: Score after repack:\nprotocols.docking.DockingProtocol: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 0.338 -1690.551 -571.406\n fa_rep 0.186 3035.584 563.647\n fa_sol 0.242 913.492 221.065\n fa_elec 0.026 -353.527 -9.192\n fa_pair 0.164 -37.809 -6.201\n hbond_sr_bb 0.245 -47.347 -11.600\n hbond_lr_bb 0.245 -100.043 -24.511\n hbond_bb_sc 0.245 -26.342 -6.454\n hbond_sc 0.245 -8.149 -1.996\n dslf_ss_dst 0.500 -15.294 -7.647\n dslf_cs_ang 2.000 1.100 2.200\n dslf_ss_dih 5.000 0.462 2.308\n dslf_ca_dih 5.000 0.254 1.269\n fa_dun 0.036 667.709 24.038\n---------------------------------------------------\n Total weighted score: 175.521\nprotocols.docking.DockMCMProtocol: in DockMCMProtocol.apply\nprotocols.docking.DockMCMProtocol: Using the DockingTaskFactory.\nprotocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockMCMCycle: /// Dockable Jumps: 1 ///\nprotocols.docking.DockMCMCycle: /// Translation: 0.1 ///\nprotocols.docking.DockMCMCycle: /// Rotation: 5 ///\nprotocols.docking.DockMCMCycle: /// Scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 0.338) (fa_rep 0.18568) (fa_sol 0.242) (fa_elec 0.026) (fa_pair 0.164) (hbond_sr_bb 0.245) (hbond_lr_bb 0.245) (hbond_bb_sc 0.245) (hbond_sc 0.245) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.036)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: /// Packing scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 0.338) (fa_rep 0.18568) (fa_sol 0.242) (fa_elec 0.026) (fa_pair 0.164) (hbond_sr_bb 0.245) (hbond_lr_bb 0.245) (hbond_bb_sc 0.245) (hbond_sc 0.245) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.036)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1214 rotamers at 38 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: P/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/demo/D100_Docking.py:95: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.rigid import (\nKilled\n\nFinished D100_Docking in 0:17:04.026527", "state": "failed"}, "D110_DNA_interface": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.4846 seconds.\ncore.import_pose.import_pose: File '../test/data/dna_test.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name O5* to O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name C5* to C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Number of nucleic acid residue fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: -12 C DG GUA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: P \ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C4'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 164 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 166 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 167 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 169 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 170 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 172 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 173 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 174 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:UpperRNA:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 175 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE:LowerDNA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 177 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 181 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 182 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 183 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 184 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 185 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 186 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT:UpperDNA\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for OP1 and OP2 for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 161\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N9 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N7 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C8 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: Connecting residues: 162 ( GUA:LowerDNA:VirtualDNAPhosphate ) and 163 ( CYT ) at atoms O3' and P \ncore.conformation.Conformation: with mutual distances: 0.293633 and 0.00610344\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 163 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 164 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 165 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 166 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 167 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 168 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 169 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 170 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 171 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 172 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 173 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 174 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 175 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 176 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 177 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 178 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 179 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 181 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 182 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 183 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 184 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 185 atom 2H2' (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 12 atom name N9 \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.676863 seconds to load from binary\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.docking.DockMCMProtocol: in DockMCMProtocol.apply\nprotocols.docking.DockMCMProtocol: Using the DockingTaskFactory.\nprotocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockMCMCycle: /// Dockable Jumps: 1 ///\nprotocols.docking.DockMCMCycle: /// Translation: 0.1 ///\nprotocols.docking.DockMCMCycle: /// Rotation: 5 ///\nprotocols.docking.DockMCMCycle: /// Scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 0.947733) (fa_rep 0.577238) (fa_sol 0.507356) (fa_elec 1) (pro_close 1) (hbond_sr_bb 2.80253) (hbond_lr_bb 2.80253) (hbond_bb_sc 2.80253) (hbond_sc 1.59624) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (fa_dun 0.68229) (p_aa_pp 0.612065) (ref 1) (res_type_constraint 1)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref -1.58548 -1.18225 3.39 1.61782 0.10405 -2.19778 0.838118 -1.81735 -1.53824 -1.26583 -1.40187 1.06144 -2.58097 -0.20752 9.93689 -2.59427 -1.18434 -1.42293 1.82099 0.209525\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: /// Packing scorefunction: ///\nprotocols.docking.DockMCMCycle: ScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockMCMCycle: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_protein_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockMCMCycle: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockMCMCycle: HbondOptions::show: mphbond: false\nprotocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockMCMCycle: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: \nprotocols.docking.DockMCMCycle: ////////////////////////////////////////////////////////////////////////////////\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 388 rotamers at 34 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nWorking on decoy: dna_output_0.pdb\ncommand line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 406 rotamers at 33 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \n\nFinished D110_DNA_interface in 0:16:30.554739", "state": "passed"}, "D120_Ligand_interface": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished D120_Ligand_interface in 0:00:37.805427", "state": "passed"}, "T000_Imports": {"log": "vector1_int[1, 2, 3, 4]\nvector1_double[1, 2, 3, 4.5]\nvector1_std_string[a, b, c, d]\nstd_set[1, 2, 3, 4]\nstd_set[1, 2, 3, 4.5]\nstd_set[a, b, c, d]\nTesting Python bindings for Rosetta...\nInit...\nPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\ndevel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88\nPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1809607912 seed_offset=0 real_seed=-1809607912\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1809607912 RG_type=mt19937\n\nFinished T000_Imports in 0:00:37.805815", "state": "passed"}, "T005_Bindings": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nTotal residues: 0\nSequence: \nFold tree:\nFOLD_TREE \nTotal residues: 0\nSequence: \nFold tree:\nFOLD_TREE \nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: false\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: false\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: false\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nrosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionOP() PASSED\nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: false\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: false\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: false\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nrosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP() PASSED\nScoreFunction::show():\nweights:\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: true\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: true\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: true\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nrosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP2() PASSED\n<pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x40264bccf0>\n<pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x40264bccf0>\n<pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x40264bccf0>\n<pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x40264bccf0>\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-128240378 seed_offset=0 real_seed=-128240378\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-128240378 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 5.58221 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T005_Bindings.py:48: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.protocols.toolbox.py_inheritance_test import *\n\nFinished T005_Bindings in 0:02:17.689343", "state": "passed"}, "T006_Options": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nout:nstruct: 5\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -nstruct 5 -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T006_Options in 0:00:37.925685", "state": "passed"}, "T007_TracerIO": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.7771 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n-------- Test/Demo for capturing Tracers output in PyRosetta --------\nPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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\nCaptured IO:\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.7771 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n\nPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nMyPyTracer.output_callback with argument:\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \n\nMyPyTracer.output_callback with argument:\n\nMyPyTracer.output_callback with argument:\ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\n\nMyPyTracer.output_callback with argument:\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\n\nMyPyTracer.output_callback with argument:\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=967267286 seed_offset=0 real_seed=967267286\n\nMyPyTracer.output_callback with argument:\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=967267286 RG_type=mt19937\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=967267286 seed_offset=0 real_seed=967267286\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=967267286 RG_type=mt19937\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T007_TracerIO.py:14: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n import rosetta, pyrosetta\n\nFinished T007_TracerIO in 0:00:48.569163", "state": "passed"}, "T008_Serialization": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-448111731 seed_offset=0 real_seed=-448111731\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-448111731 RG_type=mt19937\n\nFinished T008_Serialization in 0:00:37.802672", "state": "passed"}, "T009_Exceptions": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nExceptions type: <class 'RuntimeError'>, message: \n\nFile: /home/benchmark/rosetta/source/src/protocols/rosetta_scripts/RosettaScriptsParser.cc:514\nparser::protocol file must specify PROTOCOLS section\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1200316648 seed_offset=0 real_seed=1200316648\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1200316648 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 5.59028 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n\nFinished T009_Exceptions in 0:03:04.373067", "state": "passed"}, "T010_LoadPDB": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.48129 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.651808 seconds to load from binary\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.151932 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/EPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.io.silent.SilentFileData: Reading all structures from ../test/data/test_in.silent\ncore.io.silent.SilentFileData: Finished reading 8 structures from ../test/data/test_in.silent\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\n\nFinished T010_LoadPDB in 0:02:26.398334", "state": "passed"}, "T020_Pose_Bindings": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T020_Pose_Bindings.py:26: DeprecationWarning: Pose.__len__ is deprecated, prefer 'pose.residues.__len__'.\n assert(len(pose1) == 8) # Deprecated\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T020_Pose_Bindings.py:35: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'.\n for residue in pose1: # Deprecated\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T020_Pose_Bindings.py:56: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'.\n assert(''.join([res.annotated_name() for res in pose1[1:9]]) == 'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]') # Deprecated\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T020_Pose_Bindings.py:57: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'.\n assert(''.join([res.annotated_name() for res in pose1[-6:8]]) == 'DEFGH') # Deprecated\n\nFinished T020_Pose_Bindings in 0:00:45.323635", "state": "passed"}, "T040_Types": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T040_Types in 0:00:37.813373", "state": "passed"}, "T100_basic": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nGeneral testing ----------------------------------------------\nCreating Pose object...\nPose from PDB...\nBuilding Pose from sequence...\nPDB file name: DSEEKFLR\nTotal residues: 21\nSequence: DSEEKFLRRIGRFGYGYGPYE\nFold tree:\nFOLD_TREE EDGE 1 21 -1 \nDump PDB...\naccessing pose attributes\nPDB file name: ../test/data/test_in.pdb\nTotal residues: 116\nSequence: DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPL\nFold tree:\nFOLD_TREE EDGE 1 116 -1 \nthere are 116 residues in this pose object\nphi of residue 5 is -64.78549729348202\npsi of residue 5 is -39.71243941172726\nset phi of residue 5 to -60\nset psi of residue 5 to -50\naccessing residue 5 from pose\nResidue 5: ILE (ILE, I):\nBase: ILE\n Properties: POLYMER PROTEIN CANONICAL_AA HYDROPHOBIC ALIPHATIC BETA_BRANCHED_SIDECHAIN METALBINDING ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB CG1 CG2 CD1 HB 1HG1 2HG1 1HG2 2HG2 3HG2 1HD1 2HD1 3HD1\nAtom Coordinates:\n N : -2.53898, 36.4415, 79.2297\n CA : -1.97052, 36.1949, 80.5403\n C : -2.23109, 37.3858, 81.4325\n O : -2.50917, 37.2043, 82.6002\n CB : -0.453211, 35.963, 80.4929\n CG1: -0.175565, 34.5273, 80.077\n CG2: 0.172042, 36.261, 81.8574\n CD1: -0.927946, 33.5005, 80.9024\n H : -1.93862, 36.5194, 78.4212\n HA : -2.46732, 35.3543, 81.0219\n HB : -0.0182833, 36.6096, 79.7313\n 1HG1: -0.458733, 34.4327, 79.0287\n 2HG1: 0.8975, 34.3623, 80.1785\n 1HG2: 1.24765, 36.092, 81.8094\n 2HG2: -0.0204952, 37.2987, 82.1272\n 3HG2: -0.264762, 35.6037, 82.6097\n 1HD1: -0.681316, 32.4982, 80.5509\n 2HD1: -0.643714, 33.5961, 81.9508\n 3HD1: -2.00002, 33.6654, 80.801\nMirrored relative to coordinates in ResidueType: FALSE\n\naccessing atoms from residue 5\n-2.53898, 36.4415, 79.2297\nxyz of at5N: -2.53898489237762 36.44151978598334 79.22969355726434\nnorm of xyz at5N: <bound method PyCapsule.norm of <pyrosetta.rosetta.numeric.xyzVector_double_t object at 0x4002024e70>>\nvector1_core_conformation_Atom[-2.53898, 36.4415, 79.2297, -1.97052, 36.1949, 80.5403, -2.23109, 37.3858, 81.4325, -2.50917, 37.2043, 82.6002, -0.453211, 35.963, 80.4929, -0.175565, 34.5273, 80.077, 0.172042, 36.261, 81.8574, -0.927946, 33.5005, 80.9024, -1.93862, 36.5194, 78.4212, -2.46732, 35.3543, 81.0219, -0.0182833, 36.6096, 79.7313, -0.458733, 34.4327, 79.0287, 0.8975, 34.3623, 80.1785, 1.24765, 36.092, 81.8094, -0.0204952, 37.2987, 82.1272, -0.264762, 35.6037, 82.6097, -0.681316, 32.4982, 80.5509, -0.643714, 33.5961, 81.9508, -2.00002, 33.6654, 80.801]\nbond length of N-CA in residue 5 is \n1.4496692726273892\nbond angle of N-CA-C in residue 5 is \n1.9094258533068342\nsetting bond length of N-CA in residue 5 to 1.5A \nsetting bond angle of N-CA-C in residue 5 to 90 \npose was generated from this pdb file: ../test/data/test_in.pdb\npose numbering for chain A, residue 5, is 5\npdb chain letter and residue number for residue 5, is 5 A \nResidue 0: ALA (ALA, A):\nBase: ALA\n Properties: POLYMER PROTEIN CANONICAL_AA ALIPHATIC METALBINDING ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB 1HB 2HB 3HB \nAtom Coordinates:\n N : 0, 0, 0\n CA : 1.458, 0, 0\n C : 2.00885, 1.42017, 0\n O : 1.38304, 2.33899, -0.528697\n CB : 1.9878, -0.772763, -1.19909\n H : -0.491969, 0.763905, -0.44104\n HA : 1.79666, -0.489627, 0.91315\n 1HB : 3.07772, -0.76375, -1.18511\n 2HB : 1.63286, -1.80244, -1.15412\n 3HB : 1.63327, -0.30698, -2.11716\nMirrored relative to coordinates in ResidueType: FALSE\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.46132 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.167922 seconds.\n\nFinished T100_basic in 0:00:48.047683", "state": "passed"}, "T110_numeric": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T110_numeric in 0:00:37.880840", "state": "passed"}, "T120_core.RotamerSets": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2022319904 seed_offset=0 real_seed=-2022319904\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2022319904 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.41661 seconds.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\n\nFinished T120_core.RotamerSets in 0:02:15.379477", "state": "passed"}, "T150_PyMOL_Integration": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.4134 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/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.647796 seconds to load from binary\n\nFinished T150_PyMOL_Integration in 0:02:20.354039", "state": "passed"}, "T190_Bindings_Utility": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\n\nFinished T190_Bindings_Utility in 0:00:37.793998", "state": "passed"}, "T200_Scoring": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.44841 seconds.\ncore.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.655582 seconds to load from binary\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nScoring ----------------------------------------------\nCreating standard fullatom score function and scoring\nCreating standard centroid score function and scoring\nCreating standard score function and scoring, again\nCreating standard score from scratch\nAdjusting weights and scoring\nweight for fa_atr set to: 1.0\nScoreFunction::show():\nweights: (fa_atr 1) (fa_rep 1) (fa_pair 1)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nEnergyMethodOptions::show: mhc_epitope_setup_files: \nEnergyMethodOptions::show: netcharge_setup_files: \nEnergyMethodOptions::show: aspartimide_penalty_value: 25\nEnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nEnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nEnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nEnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nEnergyMethodOptions::show: covalent_labeling_input: \nEnergyMethodOptions::show: covalent_labeling_fa_input: \nEnergyMethodOptions::show: hrf_dynamics_input: \nEnergyMethodOptions::show: depc_ms_input: \nEnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nEnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nEnergyMethodOptions::show: exclude_monomer_fa_elec: false\nEnergyMethodOptions::show: elec_max_dis: 5.5\nEnergyMethodOptions::show: elec_min_dis: 1.6\nEnergyMethodOptions::show: elec_die: 10\nEnergyMethodOptions::show: elec_no_dis_dep_die: false\nEnergyMethodOptions::show: elec_sigmoidal_die: true\nEnergyMethodOptions::show: elec_sigmoidal_D: 80\nEnergyMethodOptions::show: elec_sigmoidal_D0: 6\nEnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nEnergyMethodOptions::show: smooth_fa_elec: true\nEnergyMethodOptions::show: grpelec_fade_type: false\nEnergyMethodOptions::show: grpelec_fade_param1: 1\nEnergyMethodOptions::show: grpelec_fade_param2: 1\nEnergyMethodOptions::show: grpelec_fade_hbond: 0\nEnergyMethodOptions::show: grp_cpfxn: 1\nEnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nEnergyMethodOptions::show: grpelec_context_dependent: 0\nEnergyMethodOptions::show: use_polarization: true\nEnergyMethodOptions::show: use_gen_kirkwood: true\nEnergyMethodOptions::show: protein_dielectric: 1\nEnergyMethodOptions::show: water_dielectric: 78.3\nEnergyMethodOptions::show: exclude_DNA_DNA: false\nEnergyMethodOptions::show: exclude_intra_res_protein: true\nEnergyMethodOptions::show: count_pair_hybrid: false\nEnergyMethodOptions::show: count_pair_full: false\nEnergyMethodOptions::show: put_intra_into_total: false\nEnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nEnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nEnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nEnergyMethodOptions::show: envsmooth_zero_negatives: false\nEnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nEnergyMethodOptions::show: pb_bound_tag: bound\nEnergyMethodOptions::show: pb_unbound_tag: unbound\nEnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nEnergyMethodOptions::show: ordered_wat_penalty: 1.221\nEnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nEnergyMethodOptions::show: nmer_ref_seq_length_: 9\nEnergyMethodOptions::show: nmer_svm_term_length_: 3\nEnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nEnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nEnergyMethodOptions::show: nmer_svm_scorecut_: 0\nEnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nEnergyMethodOptions::show: nmer_svm_aa_matrix_: \nEnergyMethodOptions::show: nmer_svm_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_list_: \nEnergyMethodOptions::show: nmer_svm_defined_: 0\nEnergyMethodOptions::show: nmer_svm_: \nEnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_list_: \nEnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nEnergyMethodOptions::show: nmer_svm_rank_: \nEnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nEnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nEnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nEnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nEnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nEnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nEnergyMethodOptions::show: hbnet_max_network_size_: 0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nEnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nEnergyMethodOptions::show: target_clash_pdb_:\nEnergyMethodOptions::show: dump_trajectory_prefix_: traj\nEnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nEnergyMethodOptions::show: dump_trajectory_stride_: 1\nEnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nEnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nHBondOptions::show: hb_max_energy: 0\nHBondOptions::show: exclude_DNA_DNA: false\nHBondOptions::show: exclude_intra_res_protein_: true\nHBondOptions::show: exclude_intra_res_RNA_: false\nHBondOptions::show: put_intra_into_total_: false\nHBondOptions::show: exclude_self_hbonds: true\nHBondOptions::show: use_hb_env_dep: true\nHBondOptions::show: use_hb_env_dep_DNA: true\nHBondOptions::show: smooth_hb_env_dep: true\nHBondOptions::show: bb_donor_acceptor_check: true\nHBondOptions::show: decompose_bb_hb_into_pair_energies: false\nHBondOptions::show: params_database_tag_: ref2015_params\nHBondOptions::show: use_sp2_chi_penalty_: true\nHBondOptions::show: sp2_BAH180_rise_: 0.75\nHBondOptions::show: sp2_outer_width_: 0.357\nHBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nHBondOptions::show: fade_energy_: 1\nHBondOptions::show: exclude_ether_oxygens_: 0\nHBondOptions::show: Mbhbond: false \nHbondOptions::show: mphbond: false\nHBondOptions::show: hbond_energy_shift: 0\nHBondOptions::show: water_hybrid_sf: false\nRNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nRNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nRNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nRNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nFreeDOF_Options::show: free_suite_bonus: -1\nFreeDOF_Options::show: free_2HOprime_bonus: -0.5\nFreeDOF_Options::show: free_sugar_bonus: -1\nFreeDOF_Options::show: pack_phosphate_penalty: 0.25\nFreeDOF_Options::show: free_side_chain_bonus: -0.5\n\n\nScore break down for pose...\nall residue energies are\nNone\nweighted energies for residue 5\nNone\n fa_atr: -0.593 fa_rep: 0.118 fa_pair: 0.000\nfa_atr of residue 5\n-0.5929040959214456\nfa_atr for residue 5: -0.5929040959214456\nmanually calculating 2body context-independent energies between residues 4 and 5\nfa_atr between 1 and 2: -0.42118788604496193\nfa_pair between 1 and 2: 0.0\nfa_rep between 1 and 2: 0.12092691972750393\nScoreType.fa_atrScoreType.fa_repScoreType.fa_solScoreType.fa_intra_atrScoreType.fa_intra_repScoreType.fa_intra_solScoreType.fa_intra_atr_xover4ScoreType.fa_intra_rep_xover4ScoreType.fa_intra_sol_xover4ScoreType.fa_intra_atr_nonproteinScoreType.fa_intra_rep_nonproteinScoreType.fa_intra_sol_nonproteinScoreType.fa_intra_RNA_base_phos_atrScoreType.fa_intra_RNA_base_phos_repScoreType.fa_intra_RNA_base_phos_solScoreType.fa_atr_dummyScoreType.fa_rep_dummyScoreType.fa_sol_dummyScoreType.fa_vdw_tinkerScoreType.lk_hackScoreType.lk_ballScoreType.lk_ball_wtdScoreType.lk_ball_isoScoreType.lk_ball_bridgeScoreType.lk_ball_bridge_uncplScoreType.lk_domeScoreType.lk_dome_isoScoreType.lk_dome_bridgeScoreType.lk_dome_bridge_uncplScoreType.lk_ball_bridge2ScoreType.lk_ball_bridge_uncpl2ScoreType.lk_dome_packScoreType.coarse_fa_atrScoreType.coarse_fa_repScoreType.coarse_fa_solScoreType.coarse_beadljScoreType.mm_lj_intra_repScoreType.mm_lj_intra_atrScoreType.mm_lj_inter_repScoreType.mm_lj_inter_atrScoreType.mm_twistScoreType.mm_bendScoreType.mm_stretchScoreType.lk_costhetaScoreType.lk_polarScoreType.lk_nonpolarScoreType.lk_polar_intra_RNAScoreType.lk_nonpolar_intra_RNAScoreType.fa_elecScoreType.fa_elec_bb_bbScoreType.fa_elec_bb_scScoreType.fa_elec_sc_scScoreType.fa_intra_elecScoreType.h2o_hbondScoreType.dna_drScoreType.dna_bpScoreType.dna_bsScoreType.dna_refScoreType.peptide_bondScoreType.pcsScoreType.pcsTs1ScoreType.pcsTs2ScoreType.pcsTs3ScoreType.pcsTs4ScoreType.pcs2ScoreType.fastsaxsScoreType.saxs_scoreScoreType.saxs_cen_scoreScoreType.saxs_fa_scoreScoreType.pddf_scoreScoreType.fiberdiffractionScoreType.fiberdiffractiondensScoreType.epr_deer_scoreScoreType.fa_mbenvScoreType.fa_mbsolvScoreType.fa_elec_rna_phos_phosScoreType.fa_elec_rna_phos_sugrScoreType.fa_elec_rna_phos_baseScoreType.fa_elec_rna_sugr_sugrScoreType.fa_elec_rna_sugr_baseScoreType.fa_elec_rna_base_baseScoreType.fa_elec_rna_phos_phos_fastScoreType.fa_elec_rna_phos_sugr_fastScoreType.fa_elec_rna_phos_base_fastScoreType.fa_elec_rna_sugr_sugr_fastScoreType.fa_elec_rna_sugr_base_fastScoreType.fa_elec_rna_base_base_fastScoreType.fa_elec_aro_aroScoreType.fa_elec_aro_allScoreType.hack_aroScoreType.rna_fa_atr_baseScoreType.rna_fa_rep_baseScoreType.rna_data_backboneScoreType.ch_bondScoreType.ch_bond_bb_bbScoreType.ch_bond_sc_scScoreType.ch_bond_bb_scScoreType.pro_closeScoreType.rama2bScoreType.vdwScoreType.cenpackScoreType.cenpack_smoothScoreType.cen_hbScoreType.hybrid_vdwScoreType.gaussScoreType.rna_vdwScoreType.rnp_vdwScoreType.rna_base_backboneScoreType.rna_backbone_backboneScoreType.rna_repulsiveScoreType.rna_base_pair_pairwiseScoreType.rna_base_axis_pairwiseScoreType.rna_base_stagger_pairwiseScoreType.rna_base_stack_pairwiseScoreType.rna_base_stack_axis_pairwiseScoreType.rna_data_baseScoreType.rna_base_pairScoreType.rna_base_axisScoreType.rna_base_staggerScoreType.rna_base_stackScoreType.rna_base_stack_axisScoreType.rnp_base_pairScoreType.rnp_stackScoreType.rnp_stack_xyScoreType.rnp_pairScoreType.rnp_pair_distScoreType.rnp_aa_to_rna_backboneScoreType.rna_mg_pointScoreType.rna_mg_point_indirectScoreType.mgScoreType.mg_ligScoreType.mg_solScoreType.mg_refScoreType.hoh_refScoreType.rna_torsionScoreType.rna_torsion_scScoreType.rna_suiteScoreType.rna_jr_suiteScoreType.suiteness_bonusScoreType.tna_suiteScoreType.rna_sugar_closeScoreType.fa_stackScoreType.fa_stack_lowerScoreType.fa_stack_upperScoreType.fa_stack_aroScoreType.fa_stack_extScoreType.fa_stack_solScoreType.fa_stack_lrScoreType.fa_stack_rna_proteinScoreType.fa_stack_rna_protein_aroScoreType.ss_contact_worstScoreType.stack_elecScoreType.stack_elec_base_baseScoreType.stack_elec_base_bbScoreType.alignmentScoreType.dna_bb_torsionScoreType.dna_sugar_closeScoreType.dna_base_distanceScoreType.geom_sol_fastScoreType.geom_sol_fast_intra_RNAScoreType.fa_cust_pair_distScoreType.custom_atom_pairScoreType.orbitals_hpol_bbScoreType.pci_cation_piScoreType.pci_pi_piScoreType.pci_salt_bridgeScoreType.pci_hbondScoreType.arg_cation_piScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_lastScoreType.pythonScoreType.fa_pairScoreType.fa_pair_aro_aroScoreType.fa_pair_aro_polScoreType.fa_pair_pol_polScoreType.hbond_sr_bbScoreType.hbond_lr_bbScoreType.hbond_bb_scScoreType.hbond_sr_bb_scScoreType.hbond_lr_bb_scScoreType.hbond_scScoreType.hbond_intraScoreType.hbond_watScoreType.wat_entropyScoreType.hbondScoreType.npd_hbond_sr_bbScoreType.npd_hbond_lr_bbScoreType.npd_hbond_bb_scScoreType.npd_hbond_sr_bb_scScoreType.npd_hbond_lr_bb_scScoreType.npd_hbond_scScoreType.npd_hbond_intraScoreType.npd_hbondScoreType.fa_grpelecScoreType.PyRosettaTwoBodyContextDependentEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaTwoBodyContextDependentEnergy_lastScoreType.interface_dd_pairScoreType.geom_solScoreType.geom_sol_intra_RNAScoreType.occ_sol_fittedScoreType.occ_sol_fitted_onebodyScoreType.occ_sol_exactScoreType.cen_rot_pairScoreType.cen_rot_pair_angScoreType.cen_rot_pair_dihScoreType.pairScoreType.cen_pair_smoothScoreType.MpairScoreType.MPPairScoreType.FaMPSolvScoreType.suckScoreType.rna_rgScoreType.rna_motifScoreType.facts_elecScoreType.facts_solvScoreType.facts_sasaScoreType.motif_dockScoreType.pointwaterScoreType.goapScoreType.goap_distScoreType.goap_angleScoreType.approximate_buried_unsat_penaltyScoreType.interchain_pairScoreType.interchain_vdwScoreType.gb_elecScoreType.multipole_elecScoreType.fa_sasaScoreType.dslf_ss_dstScoreType.dslf_cs_angScoreType.dslf_ss_dihScoreType.dslf_ca_dihScoreType.dslf_cbs_dsScoreType.dslf_fa13ScoreType.dslfc_cen_dstScoreType.dslfc_cb_dstScoreType.dslfc_angScoreType.dslfc_cb_dihScoreType.dslfc_bb_dihScoreType.dslfc_rotScoreType.dslfc_transScoreType.dslfc_RTScoreType.atom_pair_constraintScoreType.base_pair_constraintScoreType.coarse_chainbreak_constraintScoreType.constant_constraintScoreType.coordinate_constraintScoreType.angle_constraintScoreType.dihedral_constraintScoreType.big_bin_constraintScoreType.dunbrack_constraintScoreType.site_constraintScoreType.metalhash_constraintScoreType.metalbinding_constraintScoreType.rna_stub_coord_hackScoreType.bond_geometryScoreType.rna_bond_geometryScoreType.Hpol_bond_geometryScoreType.ramaScoreType.omegaScoreType.fa_dunScoreType.fa_dun_devScoreType.fa_dun_rotScoreType.fa_dun_semiScoreType.cen_rot_dunScoreType.dna_chiScoreType.p_aa_ppScoreType.p_aa_ssScoreType.yhh_planarityScoreType.hxl_torsScoreType.h2o_intraScoreType.refScoreType.ref_ncScoreType.seqdep_refScoreType.nmer_refScoreType.nmer_pssmScoreType.nmer_svmScoreType.envsmoothScoreType.e_pHScoreType.rna_bulgeScoreType.dna_dihedral_bbScoreType.dna_dihedral_chiScoreType.dna_dihedral_sugarScoreType.sugar_bbScoreType.free_suiteScoreType.free_2HOprimeScoreType.free_side_chainScoreType.free_baseScoreType.free_resScoreType.free_dofScoreType.intermolScoreType.other_poseScoreType.special_rotScoreType.PB_elecScoreType.cen_env_smoothScoreType.cbeta_smoothScoreType.cen_rot_envScoreType.cen_rot_cbetaScoreType.envScoreType.cbetaScoreType.DFIREScoreType.MenvScoreType.McbetaScoreType.Menv_non_helixScoreType.Menv_terminiScoreType.Menv_tm_projScoreType.MlipoScoreType.rgScoreType.rg_localScoreType.coScoreType.hs_pairScoreType.ss_pairScoreType.rsigmaScoreType.sheetScoreType.burial_v2ScoreType.burialScoreType.abegoScoreType.covalent_labelingScoreType.covalent_labeling_faScoreType.hrf_ms_labelingScoreType.hrf_dynamicsScoreType.ccs_immsScoreType.depc_msScoreType.rnp_envScoreType.loop_closeScoreType.missing_resScoreType.MPEnvScoreType.MPCbetaScoreType.MPLipoScoreType.MPTerminiScoreType.MPNonHelixScoreType.MPTMProjScoreType.FaMPEnvScoreType.FaMPEnvSmoothScoreType.fa_water_to_bilayerScoreType.FaMPAsymEzCBScoreType.FaMPAsymEzCGScoreType.MPResidueLipophilicityScoreType.span_insScoreType.mp_span_angScoreType.MPHelicalityScoreType.natbias_ssScoreType.natbias_hsScoreType.natbias_hhScoreType.natbias_stwistScoreType.aa_cmpScoreType.dock_ens_confScoreType.csaScoreType.dcScoreType.rdcScoreType.rdc_segmentsScoreType.rdc_rohlScoreType.nmr_pcsPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 1.000 -5.202 -5.202\n fa_rep 1.000 1.049 1.049\n fa_pair 1.000 0.000 0.000\n---------------------------------------------------\n Total weighted score: -4.153\ncore.scoring.Energies: E fa_atr fa_rep fa_pair\ncore.scoring.Energies: E(i) 1 -0.30 0.06 0.00\ncore.scoring.Energies: E(i) 2 -0.51 0.12 0.00\ncore.scoring.Energies: E(i) 3 -0.60 0.11 0.00\ncore.scoring.Energies: E(i) 4 -0.59 0.12 0.00\ncore.scoring.Energies: E(i) 5 -0.59 0.12 0.00\ncore.scoring.Energies: E(i) 6 -0.60 0.11 0.00\ncore.scoring.Energies: E(i) 7 -0.60 0.11 0.00\ncore.scoring.Energies: E(i) 8 -0.59 0.12 0.00\ncore.scoring.Energies: E(i) 9 -0.52 0.12 0.00\ncore.scoring.Energies: E(i) 10 -0.31 0.06 0.00\ncore.scoring.Energies: total_energy fa_atr -5.202\ncore.scoring.Energies: total_energy fa_rep 1.049\ncore.scoring.Energies: total_energy fa_pair 0.000\ncore.scoring.Energies: E fa_atr fa_rep fa_pair\ncore.scoring.Energies: E(i) 5 -0.59 0.12 0.00\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\ncore.scoring.hbonds.HBondSet: #A 6 HIS N A 2 ALA O 2.04 144.3 129.5 -90.7 1.000 -0.591\ncore.scoring.hbonds.HBondSet: #A 8 ILE N A 4 THR O 2.02 165.0 165.8 -132.1 1.000 -1.102\ncore.scoring.hbonds.HBondSet: #A 9 LEU N A 5 ILE O 2.26 163.0 149.7 -108.0 1.000 -0.865\ncore.scoring.hbonds.HBondSet: #A 10 ASP N A 7 SER O 1.99 118.8 121.9 -72.7 1.000 -0.053\ncore.scoring.hbonds.HBondSet: #A 11 TRP N A 7 SER O 2.13 163.6 152.7 150.3 1.000 -1.338\ncore.scoring.hbonds.HBondSet: #A 12 ILE N A 8 ILE O 2.03 139.2 140.6 -123.7 1.000 -0.721\ncore.scoring.hbonds.HBondSet: #A 13 GLU N A 9 LEU O 2.04 165.1 162.3 -156.5 1.000 -1.224\ncore.scoring.hbonds.HBondSet: #A 14 ASP N A 10 ASP O 1.86 150.2 152.5 -107.8 1.000 -0.689\ncore.scoring.hbonds.HBondSet: #A 15 ASN ND2A 11 TRP O 1.74 167.5 145.0 55.4 0.576 -1.075\ncore.scoring.hbonds.HBondSet: #A 15 ASN N A 12 ILE O 1.90 129.6 117.0 -123.3 1.000 -0.502\ncore.scoring.hbonds.HBondSet: #A 16 LEU N A 12 ILE O 2.12 139.7 156.3 41.7 1.000 -0.648\ncore.scoring.hbonds.HBondSet: #A 51 TYR OH A 13 GLU OE1 2.33 127.5 132.6 175.2 0.694 -0.057\ncore.scoring.hbonds.HBondSet: #A 55 ARG NH1A 13 GLU OE2 1.34 170.5 131.0 -58.3 0.812 -0.243\ncore.scoring.hbonds.HBondSet: #A 18 SER N A 15 ASN O 2.25 125.4 126.6 135.8 1.000 -0.507\ncore.scoring.hbonds.HBondSet: #A 56 LYS NZ A 19 PRO O 2.09 136.2 127.1 -155.2 0.835 -0.338\ncore.scoring.hbonds.HBondSet: #A 26 SER N A 22 LEU O 1.89 153.1 161.7 -159.5 1.000 -0.965\ncore.scoring.hbonds.HBondSet: #A 27 GLU N A 23 GLU O 1.90 127.2 124.4 -127.4 1.000 -0.529\ncore.scoring.hbonds.HBondSet: #A 28 ARG N A 24 LYS O 2.13 151.6 161.0 139.1 1.000 -0.876\ncore.scoring.hbonds.HBondSet: #A 30 GLY N A 28 ARG O 2.49 110.6 116.7 -151.7 1.000 -0.033\ncore.scoring.hbonds.HBondSet: #A 35 HIS N A 32 SER OG 2.29 149.9 129.3 42.4 0.412 -1.133\ncore.scoring.hbonds.HBondSet: #A 36 LEU N A 32 SER O 2.00 150.7 167.4 51.1 1.000 -0.802\ncore.scoring.hbonds.HBondSet: #A 37 GLN N A 33 LYS O 2.10 152.4 144.0 -111.3 1.000 -0.862\ncore.scoring.hbonds.HBondSet: #A 38 ARG N A 34 TRP O 2.05 155.6 134.2 -129.9 1.000 -1.268\ncore.scoring.hbonds.HBondSet: #A 39 MET N A 35 HIS O 1.83 162.3 167.2 121.8 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #A 40 PHE N A 36 LEU O 2.00 162.8 150.8 -90.5 1.000 -1.000\ncore.scoring.hbonds.HBondSet: #A 41 LYS N A 37 GLN O 1.92 156.7 151.5 -106.1 1.000 -0.897\ncore.scoring.hbonds.HBondSet: #A 42 LYS N A 38 ARG O 2.04 174.7 160.8 -124.7 1.000 -1.211\ncore.scoring.hbonds.HBondSet: #A 43 GLU N A 39 MET O 1.81 133.8 142.7 -148.9 1.000 -0.720\ncore.scoring.hbonds.HBondSet: #A 44 THR N A 40 PHE O 1.84 148.2 139.0 -104.0 1.000 -0.626\ncore.scoring.hbonds.HBondSet: #A 46 HIS N A 44 THR OG1 2.38 140.9 115.1 31.0 0.647 -0.563\ncore.scoring.hbonds.HBondSet: #A 51 TYR N A 47 SER O 2.31 143.2 157.6 -134.7 1.000 -0.475\ncore.scoring.hbonds.HBondSet: #A 52 ILE N A 48 LEU O 2.04 169.5 172.7 -140.4 1.000 -1.110\ncore.scoring.hbonds.HBondSet: #A 53 ARG N A 49 GLY O 2.27 160.5 141.5 -138.6 1.000 -1.219\ncore.scoring.hbonds.HBondSet: #A 54 SER N A 50 GLN O 2.03 139.9 119.8 -107.0 1.000 -0.580\ncore.scoring.hbonds.HBondSet: #A 55 ARG N A 51 TYR O 1.91 145.7 149.7 -119.9 1.000 -0.733\ncore.scoring.hbonds.HBondSet: #A 56 LYS N A 52 ILE O 2.05 152.8 145.5 -144.7 1.000 -1.268\ncore.scoring.hbonds.HBondSet: #A 57 MET N A 53 ARG O 1.90 161.7 154.0 -106.5 1.000 -0.970\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 54 SER O 2.05 153.5 133.7 -110.9 1.000 -0.941\ncore.scoring.hbonds.HBondSet: #A 59 GLU N A 55 ARG O 2.06 152.9 137.4 -113.4 1.000 -0.939\ncore.scoring.hbonds.HBondSet: #A 55 ARG NE A 113 LEU O 2.13 147.9 119.9 -95.9 0.859 -0.450\ncore.scoring.hbonds.HBondSet: #A 55 ARG NH2A 113 LEU O 1.82 143.4 172.4 178.3 0.859 -0.454\ncore.scoring.hbonds.HBondSet: #A 60 ILE N A 56 LYS O 1.92 158.0 145.1 -109.1 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 56 LYS NZ A 78 TYR O 1.99 147.6 161.9 -149.3 0.976 -0.347\ncore.scoring.hbonds.HBondSet: #A 61 ALA N A 57 MET O 2.19 141.3 144.0 -107.9 1.000 -0.481\ncore.scoring.hbonds.HBondSet: #A 62 GLN N A 58 THR O 2.32 147.4 145.9 -134.5 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #A 63 LYS N A 59 GLU O 2.38 148.8 139.1 -123.6 1.000 -0.599\ncore.scoring.hbonds.HBondSet: #A 78 TYR OH A 59 GLU OE1 2.33 163.0 127.0 55.3 0.882 -0.201\ncore.scoring.hbonds.HBondSet: #A 64 LEU N A 60 ILE O 2.21 144.1 134.6 -117.2 1.000 -0.669\ncore.scoring.hbonds.HBondSet: #A 66 GLU N A 62 GLN O 2.15 126.2 128.1 -135.5 1.000 -0.625\ncore.scoring.hbonds.HBondSet: #A 102 ARG NH1A 64 LEU O 2.20 150.3 103.2 -43.0 0.859 -0.641\ncore.scoring.hbonds.HBondSet: #A 69 GLU N A 67 SER OG 1.98 163.8 131.5 73.0 0.459 -2.039\ncore.scoring.hbonds.HBondSet: #A 77 ARG NH2A 69 GLU OE1 2.08 111.0 127.8 164.8 0.600 -0.556\ncore.scoring.hbonds.HBondSet: #A 102 ARG NH2A 69 GLU O 1.73 172.3 129.2 104.5 0.647 -0.841\ncore.scoring.hbonds.HBondSet: #A 74 LEU N A 70 PRO O 2.10 138.8 143.2 -162.9 1.000 -1.132\ncore.scoring.hbonds.HBondSet: #A 75 ALA N A 71 ILE O 1.85 153.0 140.3 -108.4 1.000 -0.788\ncore.scoring.hbonds.HBondSet: #A 76 GLU N AScoreType.nmr_rdcScoreType.nmr_preScoreType.cen_pair_motifsScoreType.cen_pair_motif_degreeScoreType.holesScoreType.holes_decoyScoreType.holes_reslScoreType.holes_minScoreType.holes_min_meanScoreType.rna_chem_shiftScoreType.rna_chem_mapScoreType.rna_chem_map_loresScoreType.rna_partitionScoreType.dab_sasaScoreType.dab_sevScoreType.saScoreType.d2h_saScoreType.ProQMScoreType.ProQScoreType.interchain_envScoreType.interchain_contactScoreType.chainbreakScoreType.linear_chainbreakScoreType.overlap_chainbreakScoreType.distance_chainbreakScoreType.dof_constraintScoreType.branch_connScoreType.linear_branch_connScoreType.rama_preproScoreType.paa_abego3ScoreType.cart_bondedScoreType.cart_bonded_angleScoreType.cart_bonded_lengthScoreType.cart_bonded_ringScoreType.cart_bonded_torsionScoreType.cart_bonded_properScoreType.cart_bonded_improperScoreType.gen_bondedScoreType.gen_bonded_bondScoreType.gen_bonded_angleScoreType.gen_bonded_torsionScoreType.gen_bonded_improperScoreType.neigh_vectScoreType.neigh_countScoreType.neigh_vect_rawScoreType.symE_bonusScoreType.sym_ligScoreType.mhc_epitopeScoreType.pack_statScoreType.rmsScoreType.res_type_constraintScoreType.res_type_linking_constraintScoreType.pocket_constraintScoreType.backbone_stub_constraintScoreType.backbone_stub_linear_constraintScoreType.surfaceScoreType.p_aaScoreType.unfoldedScoreType.split_unfolded_two_bodyScoreType.fa_atr_refScoreType.fa_rep_refScoreType.fa_sol_refScoreType.fa_elec_refScoreType.hbond_refScoreType.dslf_fa13_refScoreType.fa_intra_atr_refScoreType.fa_intra_rep_refScoreType.fa_intra_sol_refScoreType.pro_close_refScoreType.fa_dun_refScoreType.fa_dun_dev_refScoreType.fa_dun_rot_refScoreType.fa_dun_semi_refScoreType.rama_refScoreType.p_aa_pp_refScoreType.omega_refScoreType.mm_lj_intra_rep_refScoreType.mm_lj_intra_atr_refScoreType.mm_twist_refScoreType.elec_dens_fastScoreType.elec_dens_windowScoreType.elec_dens_whole_structure_caScoreType.elec_dens_whole_structure_allatomScoreType.elec_dens_atomwiseScoreType.grid_vdwScoreType.xtal_mlScoreType.xtal_rworkScoreType.xtal_rfreeScoreType.hpatchScoreType.Menv_smoothScoreType.wat_desolvScoreType.ring_closeScoreType.aa_repeatScoreType.aa_compositionScoreType.aspartimide_penaltyScoreType.hbnetScoreType.buried_unsatisfied_penaltyScoreType.netchargeScoreType.voids_penaltyScoreType.sap_constraintScoreType.dna_envScoreType.dna_pairScoreType.dump_trajectoryScoreType.PyRosettaEnergy_firstScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.???ScoreType.PyRosettaEnergy_lastScoreType.sidechain_neighborsScoreType.target_clashScoreType.membrane_span_constraintScoreType.membrane_span_term_z_constraintScoreType.aromatic_restraintScoreType.rna_coarse_distScoreType.total_scoreScoreType.dummy_score_type\nidentifying hydrogen bonds in structure\n 72 LEU O 2.12 179.0 157.2 -97.9 1.000 -1.108\ncore.scoring.hbonds.HBondSet: #A 77 ARG N A 73 TYR O 2.25 145.4 127.3 -111.3 1.000 -0.591\ncore.scoring.hbonds.HBondSet: #A 78 TYR N A 74 LEU O 2.27 139.7 142.0 -109.7 1.000 -0.357\ncore.scoring.hbonds.HBondSet: #A 80 PHE N A 75 ALA O 1.93 151.5 158.1 109.3 1.000 -0.785\ncore.scoring.hbonds.HBondSet: #A 85 THR N A 82 SER OG 2.28 168.9 144.9 9.5 0.482 -0.986\ncore.scoring.hbonds.HBondSet: #A 86 LEU N A 82 SER O 2.39 154.0 131.8 -121.2 1.000 -0.707\ncore.scoring.hbonds.HBondSet: #A 87 THR N A 83 GLN O 1.58 162.4 157.0 -131.4 1.000 -0.163\ncore.scoring.hbonds.HBondSet: #A 88 ARG N A 84 GLN O 1.93 164.6 148.5 -104.7 1.000 -1.041\ncore.scoring.hbonds.HBondSet: #A 89 THR N A 85 THR O 2.15 160.7 139.8 -119.7 1.000 -1.116\ncore.scoring.hbonds.HBondSet: #A 90 PHE N A 86 LEU O 1.84 164.3 149.9 -87.9 1.000 -0.895\ncore.scoring.hbonds.HBondSet: #A 91 LYS N A 87 THR O 2.05 156.2 143.4 -111.4 1.000 -0.976\ncore.scoring.hbonds.HBondSet: #A 92 ASN N A 88 ARG O 2.11 145.3 137.3 -113.7 1.000 -0.732\ncore.scoring.hbonds.HBondSet: #A 93 TYR N A 89 THR O 2.20 132.5 141.4 -131.1 1.000 -0.528\ncore.scoring.hbonds.HBondSet: #A 93 TYR N A 90 PHE O 2.17 133.3 101.2 -94.2 1.000 -0.015\ncore.scoring.hbonds.HBondSet: #A 94 PHE N A 90 PHE O 1.91 148.0 158.2 -147.9 1.000 -0.887\ncore.scoring.hbonds.HBondSet: #A 95 ASP N A 91 LYS O 1.86 129.3 118.4 -77.4 1.000 -0.164\ncore.scoring.hbonds.HBondSet: #A 93 TYR OH A 111 ARG O 1.83 153.2 166.2 98.5 0.624 -0.510\ncore.scoring.hbonds.HBondSet: #A 111 ARG NH1A 93 TYR O 2.39 132.6 132.2 -117.9 0.624 -0.001\ncore.scoring.hbonds.HBondSet: #A 111 ARG NH1A 95 ASP OD2 1.88 140.2 140.4 -85.8 0.435 -0.369\ncore.scoring.hbonds.HBondSet: #A 111 ARG NH2A 95 ASP OD2 1.97 137.7 130.0 27.8 0.435 -1.037\ncore.scoring.hbonds.HBondSet: #A 101 TYR N A 97 PRO O 2.06 151.2 145.9 -135.7 1.000 -1.111\ncore.scoring.hbonds.HBondSet: #A 102 ARG N A 98 PRO O 2.03 134.2 138.7 -133.9 1.000 -0.762\ncore.scoring.hbonds.HBondSet: #A 103 MET N A 99 HIS O 2.13 143.0 152.2 -153.1 1.000 -0.914\ncore.scoring.hbonds.HBondSet: #A 112 PHE N A 109 GLU O 2.04 153.8 151.0 -144.0 1.000 -1.177\ncore.scoring.hbonds.HBondSet: #A 114 HIS NE2A 109 GLU OE2 2.35 163.9 126.7 64.4 0.388 -0.463\ncore.scoring.hbonds.HBondSet: #A 116 LEU N A 114 HIS O 1.65 145.1 121.9 -164.6 1.000 -1.004\n\nFinished T200_Scoring in 0:02:26.346951", "state": "passed"}, "T201_Scoring_pre_talaris": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -restore_pre_talaris_2013_behavior -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1389327768 seed_offset=0 real_seed=1389327768\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1389327768 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 74 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.532321 seconds.\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp\nbasic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack library took 0.211919 seconds to load from binary\n\nFinished T201_Scoring_pre_talaris in 0:01:58.946627", "state": "passed"}, "T220_AtomAtomPairEnergies": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.48515 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: current variant for 1 CYS\ncore.conformation.Conformation: current variant for 119 CYS\ncore.conformation.Conformation: current variant for 1 CYD\ncore.conformation.Conformation: current variant for 119 CYD\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 56 CYS\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: current variant for 56 CYD\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: current variant for 133 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 133 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: current variant for 161 CYS\ncore.conformation.Conformation: current variant for 175 CYS\ncore.conformation.Conformation: current variant for 161 CYD\ncore.conformation.Conformation: current variant for 175 CYD\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.conformation.Conformation: current variant for 184 CYS\ncore.conformation.Conformation: current variant for 213 CYS\ncore.conformation.Conformation: current variant for 184 CYD\ncore.conformation.Conformation: current variant for 213 CYD\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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\n\nPrinting individual energies:\nres-res atr score emap: -2.5584311767440906\nres-res atr score pairwise: -2.5584311767440906\nres-res rep score emap: 3.515015877828057\nres-res rep score pairwise: 3.515015877828057\nres-res solv score emap: 0.7697815585356838\nres-res solv score pairwise: 0.7697815585356838\nChecking if scores match...\nScore did match, yay...\n( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.663788 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished T220_AtomAtomPairEnergies in 0:02:35.162995", "state": "passed"}, "T250_Constraints": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nconstraints ----------------------------------------------\n\nScore before constraints applied: 949.3120641217321\nScore after constraints applied: 1195.812274899854\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.43733 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.647297 seconds to load from binary\n\nFinished T250_Constraints in 0:02:24.610376", "state": "passed"}, "T300_PyJobDistributor": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nWorking on decoy: _jd_test_7.pdb\nWorking on decoy: _jd_test_8.pdb\nWorking on decoy: _jd_test_9.pdb\nWorking on decoy: _jd_test_1.pdb\nWorking on decoy: _jd_test_2.pdb\nWorking on decoy: _jd_test_3.pdb\nWorking on decoy: _jd_test_0.pdb\nWorking on decoy: _jd_test_5.pdb\nWorking on decoy: _jd_test_4.pdb\nWorking on decoy: _jd_test_6.pdb\nWorking on decoy: _jd_at_test_9.pdb.gz\nWorking on decoy: _jd_at_test_6.pdb.gz\nWorking on decoy: _jd_at_test_5.pdb.gz\nWorking on decoy: _jd_at_test_3.pdb.gz\nWorking on decoy: _jd_at_test_0.pdb.gz\nWorking on decoy: _jd_at_test_8.pdb.gz\nWorking on decoy: _jd_at_test_2.pdb.gz\nWorking on decoy: _jd_at_test_1.pdb.gz\nWorking on decoy: _jd_at_test_4.pdb.gz\nWorking on decoy: _jd_at_test_7.pdb.gz\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 5.58648 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.647823 seconds to load from binary\n\nFinished T300_PyJobDistributor in 0:02:20.139782", "state": "passed"}, "T400_Refinement": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.41357 seconds.\ncore.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10\ncore.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10\n resnum BB CHI NU BRANCH\n 001 TRUE FALSE FALSE FALSE\n 002 TRUE FALSE FALSE FALSE\n 003 TRUE FALSE FALSE FALSE\n 004 TRUE FALSE FALSE FALSE\n 005 TRUE FALSE FALSE FALSE\n 006 TRUE FALSE FALSE FALSE\n 007 TRUE FALSE FALSE FALSE\n 008 TRUE FALSE FALSE FALSE\n 009 TRUE FALSE FALSE FALSE\n 010 FALSE FALSE FALSE FALSE\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments\ncore.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.671796 seconds to load from binary\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 23.6488 23.6488\nprotocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820\nprotocols.moves.MonteCarlo: MC: 1 23.6488 23.6488 23.6488 23.6488 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database filePyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nRefinement ----------------------------------------------\nsetting up a move map\nsetting all backbone movement to true, and residue 10 to false\noutputting movemap\nmover: ClassicFragmentMover, 3mer\nCreating standard score function with patch and scoring\nmover: SmallMover\nMover name: Small, Mover type: SmallMover, Mover current tag:NoTag\nMax angle for helices (H): 0\nMax angle for strands (E): 5\nMax angle for loops (L): 50\nTemperature factor (kT): 0.5\nNumber of moves: 1\n\nmover: ShearMover\nMover name: Shear, Mover type: ShearMover, Mover current tag:NoTag\nMax angle for helices (H): 0\nMax angle for strands (E): 50\nMax angle for loops (L): 6\nTemperature factor (kT): 0.5\nNumber of moves: 1\n\nmover: MinMover\nmover: MonteCarlo\nprotocols.moves.MonteCarlo:\n\"Temperature\" (kT): 1\nTotal Trials: 4\nLowest Score: 23.6488\nLast Accepted Score: 23.6488\nlast_accept = 23.6488\n\nmover: SequenceMover\nmover: TrialMover\n opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt\nbasic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt\ncore.scoring.AtomVDW: Openning alternative vdw file: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/chemical/atom_type_sets/centroid_rot//min.txt\ncore.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN\nprotocols.TrialMover: Acceptance rate: 1\nprotocols.moves.MonteCarlo: MC: 1 22.6785 22.6785 22.6785 22.6785 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: ClassicFragmentM trials= 1; accepts= 1.0000; energy_drop/trial= -0.97029\nprotocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820\n\nFinished T400_Refinement in 0:02:49.085743", "state": "passed"}, "T500_Packing": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.46524 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\ncore.pack.task: Packer task: initialize from command line() \nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.655713 seconds to load from binary\ncore.pack.pack_rotamers: built 2848 rotamers at 115 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.pack_rotamers: built 1023 rotamers at 6 positions.\ncore.pack.interaction_graph.interactPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nPacking and Design ----------------------------------------------\nmover: PackRotamersMover\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tASP:NtermProteinFull\n2\tTRUE\tFALSE\tALA\n3\tTRUE\tFALSE\tILE\n4\tTRUE\tFALSE\tTHR\n5\tFALSE\tFALSE\t\n6\tTRUE\tFALSE\tHIS,HIS_D\n7\tTRUE\tFALSE\tSER\n8\tTRUE\tFALSE\tILE\n9\tTRUE\tFALSE\tLEU\n10\tTRUE\tFALSE\tASP\n11\tTRUE\tFALSE\tTRP\n12\tTRUE\tFALSE\tILE\n13\tTRUE\tFALSE\tGLU\n14\tTRUE\tFALSE\tASP\n15\tTRUE\tFALSE\tASN\n16\tTRUE\tFALSE\tLEU\n17\tTRUE\tFALSE\tGLU\n18\tTRUE\tFALSE\tSER\n19\tTRUE\tFALSE\tPRO\n20\tTRUE\tFALSE\tLEU\n21\tTRUE\tFALSE\tSER\n22\tTRUE\tFALSE\tLEU\n23\tTRUE\tFALSE\tGLU\n24\tTRUE\tFALSE\tLYS\n25\tTRUE\tFALSE\tVAL\n26\tTRUE\tFALSE\tSER\n27\tTRUE\tFALSE\tGLU\n28\tTRUE\tFALSE\tARG\n29\tTRUE\tFALSE\tSER\n30\tTRUE\tFALSE\tGLY\n31\tTRUE\tFALSE\tTYR\n32\tTRUE\tFALSE\tSER\n33\tTRUE\tFALSE\tLYS\n34\tTRUE\tFALSE\tTRP\n35\tTRUE\tFALSE\tHIS,HIS_D\n36\tTRUE\tFALSE\tLEU\n37\tTRUE\tFALSE\tGLN\n38\tTRUE\tFALSE\tARG\n39\tTRUE\tFALSE\tMET\n40\tTRUE\tFALSE\tPHE\n41\tTRUE\tFALSE\tLYS\n42\tTRUE\tFALSE\tLYS\n43\tTRUE\tFALSE\tGLU\n44\tTRUE\tFALSE\tTHR\n45\tTRUE\tFALSE\tGLY\n46\tTRUE\tFALSE\tHIS,HIS_D\n47\tTRUE\tFALSE\tSER\n48\tTRUE\tFALSE\tLEU\n49\tTRUE\tFALSE\tGLY\n50\tTRUE\tFALSE\tGLN\n51\tTRUE\tFALSE\tTYR\n52\tTRUE\tFALSE\tILE\n53\tTRUE\tFALSE\tARG\n54\tTRUE\tFALSE\tSER\n55\tTRUE\tFALSE\tARG\n56\tTRUE\tFALSE\tLYS\n57\tTRUE\tFALSE\tMET\n58\tTRUE\tFALSE\tTHR\n59\tTRUE\tFALSE\tGLU\n60\tTRUE\tFALSE\tILE\n61\tTRUE\tFALSE\tALA\n62\tTRUE\tFALSE\tGLN\n63\tTRUE\tFALSE\tLYS\n64\tTRUE\tFALSE\tLEU\n65\tTRUE\tFALSE\tLYS\n66\tTRUE\tFALSE\tGLU\n67\tTRUE\tFALSE\tSER\n68\tTRUE\tFALSE\tASN\n69\tTRUE\tFALSE\tGLU\n70\tTRUE\tFALSE\tPRO\n71\tTRUE\tFALSE\tILE\n72\tTRUE\tFALSE\tLEU\n73\tTRUE\tFALSE\tTYR\n74\tTRUE\tFALSE\tLEU\n75\tTRUE\tFALSE\tALA\n76\tTRUE\tFALSE\tGLU\n77\tTRUE\tFALSE\tARG\n78\tTRUE\tFALSE\tTYR\n79\tTRUE\tFALSE\tGLY\n80\tTRUE\tFALSE\tPHE\n81\tTRUE\tFALSE\tGLU\n82\tTRUE\tFALSE\tSER\n83\tTRUE\tFALSE\tGLN\n84\tTRUE\tFALSE\tGLN\n85\tTRUE\tFALSE\tTHR\n86\tTRUE\tFALSE\tLEU\n87\tTRUE\tFALSE\tTHR\n88\tTRUE\tFALSE\tARG\n89\tTRUE\tFALSE\tTHR\n90\tTRUE\tFALSE\tPHE\n91\tTRUE\tFALSE\tLYS\n92\tTRUE\tFALSE\tASN\n93\tTRUE\tFALSE\tTYR\n94\tTRUE\tFALSE\tPHE\n95\tTRUE\tFALSE\tASP\n96\tTRUE\tFALSE\tVAL\n97\tTRUE\tFALSE\tPRO\n98\tTRUE\tFALSE\tPRO\n99\tTRUE\tFALSE\tHIS,HIS_D\n100\tTRUE\tFALSE\tLYS\n101\tTRUE\tFALSE\tTYR\n102\tTRUE\tFALSE\tARG\n103\tTRUE\tFALSE\tMET\n104\tTRUE\tFALSE\tTHR\n105\tTRUE\tFALSE\tASN\n106\tTRUE\tFALSE\tMET\n107\tTRUE\tFALSE\tGLN\n108\tTRUE\tFALSE\tGLY\n109\tTRUE\tFALSE\tGLU\n110\tTRUE\tFALSE\tSER\n111\tTRUE\tFALSE\tARG\n112\tTRUE\tFALSE\tPHE\n113\tTRUE\tFALSE\tLEU\n114\tTRUE\tFALSE\tHIS,HIS_D\n115\tTRUE\tFALSE\tPRO\n116\tTRUE\tFALSE\tLEU:CtermProteinFull\n\nMover name: PackRotamersMover, Mover type: PackRotamersMover, Mover current tag:NoTag\nScore function: ref2015\n\n#Packer_Task\n\nThreads to request: ALL AVAILABLE\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tTRUE\tALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull\n2\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n3\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n4\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n5\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n6\tTRUE\tTRUE\tALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR\n7\tFALSE\tFALSE\t\n8\tFALSE\tFALSE\t\n9\tFALSE\tFALSE\t\n10\tFALSE\tFALSE\t\n11\tFALSE\tFALSE\t\n12\tFALSE\tFALSE\t\n13\tFALSE\tFALSE\t\n14\tFALSE\tFALSE\t\n15\tFALSE\tFALSE\t\n16\tFALSE\tFALSE\t\n17\tFALSE\tFALSE\t\n18\tFALSE\tFALSE\t\n19\tFALSE\tFALSE\t\n20\tFALSE\tFALSE\t\n21\tFALSE\tFALSE\t\n22\tFALSE\tFALSE\t\n23\tFALSE\tFALSE\t\n24\tFALSE\tFALSE\t\n25\tFALSE\tFALSE\t\n26\tFALSE\tFALSE\t\n27\tFALSE\tFALSE\t\n28\tFALSE\tFALSE\t\n29\tFALSE\tFALSE\t\n30\tFALSE\tFALSE\t\n31\tFALSE\tFALSE\t\n32\tFALSE\tFALSE\t\n33\tFALSE\tFALSE\t\n34\tFALSE\tFALSE\t\n35\tFALSE\tFALSE\t\n36\tFALSE\tFALSE\t\n37\tFALSE\tFALSE\t\n38\tFALSE\tFALSE\t\n39\tFALSE\tFALSE\t\n40\tFALSE\tFALSE\t\n41\tFALSE\tFALSE\t\n42\tFALSE\tFALSE\t\n43\tFALSE\tFALSE\t\n44\tFALSE\tFALSE\t\n45\tFALSE\tFALSE\t\n46\tFALSE\tFALSE\t\n47\tFALSE\tFALSE\t\n48\tFALSE\tFALSE\t\n49\tFALSE\tFALSE\t\n50\tFALSE\tFALSE\t\n51\tFALSE\tFALSE\t\n52\tFALSE\tFALSE\t\n53\tFALSE\tFALSE\t\n54\tFALSE\tFALSE\t\n55\tFALSE\tFALSE\t\n56\tFALSE\tFALSE\t\n57\tFALSE\tFALSE\t\n58\tFALSE\tFALSE\t\n59\tFALSE\tFALSE\t\n60\tFALSE\tFALSE\t\n61\tFALSE\tFALSE\t\n62\tFALSE\tFALSE\t\n63\tFALSE\tFALSE\t\n64\tFALSE\tFALSE\t\n65\tFALSE\tFALSE\t\n66\tFALSE\tFALSE\t\n67\tFALSE\tFALSE\t\n68\tFALSE\tFALSE\t\n69\tFALSE\tFALSE\t\n70\tFALSE\tFALSE\t\n71\tFALSE\tFALSE\t\n72\tFALSE\tFALSE\t\n73\tFALSE\tFALSE\t\n74\tFALSE\tFALSE\t\n75\tFALSE\tFALSE\t\n76\tFALSE\tFALSE\t\n77\tFALSE\tFALSE\t\n78\tFALSE\tFALSE\t\n79\tFALSE\tFALSE\t\n80\tFALSE\tFALSE\t\n81\tFALSE\tFALSE\t\n82\tFALSE\tFALSE\t\n83\tFALSE\tFALSE\t\n84\tFALSE\tFALSE\t\n85\tFALSE\tFALSE\t\n86\tFALSE\tFALSE\t\n87\tFALSE\tFALSE\t\n88\tFALSE\tFALSE\t\n89\tFALSE\tFALSE\t\n90\tFALSE\tFALSE\t\n91\tFALSE\tFALSE\t\n92\tFALSE\tFALSE\t\n93\tFALSE\tFALSE\t\n94\tFALSE\tFALSE\t\n95\tFALSE\tFALSE\t\n96\tFALSE\tFALSE\t\n97\tFALSE\tFALSE\t\n98\tFALSE\tFALSE\t\n99\tFALSE\tFALSE\t\n100\tFALSE\tFALSE\t\n101\tFALSE\tFALSE\t\n102\tFALSE\tFALSE\t\n103\tFALSE\tFALSE\t\n104\tFALSE\tFALSE\t\n105\tFALSE\tFALSE\t\n106\tFALSE\tFALSE\t\n107\tFALSE\tFALSE\t\n108\tFALSE\tFALSE\t\n109\tFALSE\tFALSE\t\n110\tFALSE\tFALSE\t\n111\tFALSE\tFALSE\t\n112\tFALSE\tFALSE\t\n113\tFALSE\tFALSE\t\n114\tFALSE\tFALSE\t\n115\tFALSE\tFALSE\t\n116\tFALSE\tFALSE\t\n\nGGGG\nion_graph_factory: Instantiating PDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 2822 rotamers at 115 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.minimization_packing.PackRotamersMover: [ WARNING ] undefined ScoreFunction -- creating a default one\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 4 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\n\nFinished T500_Packing in 0:06:51.141328", "state": "passed"}, "T600_Docking": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.43326 seconds.\ncore.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA \ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2\ncore.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1\ncore.conformation.Conformation: Found disulfide between residues 1 119\ncore.conformation.Conformation: current variant for 1 CYS\ncore.conformation.Conformation: current variant for 119 CYS\ncore.conformation.Conformation: current variant for 1 CYD\ncore.conformation.Conformation: current variant for 119 CYD\ncore.conformation.Conformation: Found disulfide between residues 40 56\ncore.conformation.Conformation: current variant for 40 CYS\ncore.conformation.Conformation: current variant for 56 CYS\ncore.conformation.Conformation: current variant for 40 CYD\ncore.conformation.Conformation: current variant for 56 CYD\ncore.conformation.Conformation: Found disulfide between residues 133 194\ncore.conformation.Conformation: current variant for 133 CYS\ncore.conformation.Conformation: current variant for 194 CYS\ncore.conformation.Conformation: current variant for 133 CYD\ncore.conformation.Conformation: current variant for 194 CYD\ncore.conformation.Conformation: Found disulfide between residues 161 175\ncore.conformation.Conformation: current variant for 161 CYS\ncore.conformation.Conformation: current variant for 175 CYS\ncore.conformation.Conformation: current variant for 161 CYD\ncore.conformation.Conformation: current variant for 175 CYD\ncore.conformation.Conformation: Found disulfide between residues 184 213\ncore.conformation.Conformation: current variant for 184 CYS\ncore.conformation.Conformation: current variant for 213 CYS\ncore.conformation.Conformation: current variant for 184 CYD\ncore.conformation.Conformation: current variant for 213 CYD\ncore.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 196 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1\ncore.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1\ncore.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB \ncore.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.651807 seconds to load from binary\ncore.pack.pack_rotamers: built 238 rotamers at 16 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.204801 seconds.\nprotocols.moves.RigidBodyMover: Spin: Jump (before): RT -0.389931 0.810342 -0.437379 -0.892411 -0.449663 -0.0375013 -0.227062 0.375699 0.898495 -12.6138 -39.3747 8.5794 \nprotocols.moves.RigidBodyMover: Spin: Rot (before): 40.7713 27.6633 9.48574\nprotocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.106732 -0.00891842 -0.994248 -0.993895 0.0271569 -0.106937 0.0279544 0.999591 -0.00596546 -11.6523 -39.1223 10.5884 \nprotocols.moves.RigidBodyMover: Spin: Rot (after): 40.7713 27.6633 9.48574\nprotocols.moves.RigidBodyMover: Spin: ---\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nprotocols.docking.DockingInitialPerturbation: sliding into contact\nprotocols.docking.DockingInitialPerturbation: Moving away\nprotocols.docking.DockingInitialPerturbation: Moving together\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.36\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.16\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.2\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.22\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.22\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.12\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nDocking ----------------------------------------------------\nRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.24\n\nFinished T600_Docking in 0:03:13.198935", "state": "passed"}, "T650_LoopsKIC": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -run:test_cycles True -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.38055 seconds.\ncore.import_pose.import_pose: File '../test/data/2cpl_min.pdb' automatically determined to be of type PDB\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nprotocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 144 -1 EDGE 144 150 -1 EDGE 144 156 1 EDGE 156 151 -1 EDGE 156 164 -1 \ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.147934 seconds.\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 3\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 150 BB 2\ncore.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree.\ncore.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 151 BB 1\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/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.68377 seconds to load from binary\ncore.pack.pack_rotamers: built 1918 rotamers at 164 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine init temp: 1.5\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine final temp: 0.5\ncore.pack.task: Packer task: initialize from command line() \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: Not designing\ncore.pack.pack_rotamers: built 1135 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -368.051 -368.051\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 1 -368.051\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 1/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 0.957449\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -368.397\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.65343\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -396.537\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 2/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/3 3/3 \ncore.pack.pack_rotamers: built 996 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -397.65\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -397.664 -397.664\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -397.664\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 2 -397.384\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 1/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.66148\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -397.876\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (oPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nLOOP start: 145 stop: 155 cut: 150 size: 11 skip rate: 0 extended?: False\n\nFOLD_TREE EDGE 1 144 -1 EDGE 144 150 -1 EDGE 144 156 1 EDGE 156 151 -1 EDGE 156 164 -1 \nsetting up movers\nbuilding random loop conformation with ideal bond lengths, bond angles,\nand omega angles using KIC\n attempt 0...succeeded.\ncentroid stage loop KIC remodeling\ncentroid stage loop rmsd to starting loop: 6.505196\nhigh-res KIC refinement\noutputting decoy .test_kic.pdb\nuter/inner): 2/3 2/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/3 3/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.67127\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -397.511\ncore.pack.pack_rotamers: built 996 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -397.511\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -397.531 -397.876\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -397.531\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 3 -397.628\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 1/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 1.6546\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -397.807\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 2/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/3 3/3 \nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 1.6551\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -398.034\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.65604\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -398.013\ncore.pack.pack_rotamers: built 997 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -398.013\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -398.039 -398.039\nprotocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -398.039\nprotocols.moves.TrialCounter: kic_refine_r1 trials= 8; accepts= 0.3750; energy_drop/trial= -0.09400\nprotocols.moves.TrialCounter: kic_refine_r2 trials= 9; accepts= 0.4444; energy_drop/trial= -3.13841\nprotocols.moves.TrialCounter: repack trials= 4; accepts= 1.0000; energy_drop/trial= -62.28744\n\nFinished T650_LoopsKIC in 0:11:11.850652", "state": "passed"}, "T660_LoopBuilding": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.42859 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nprotocols.loops.loops_main: [ WARNING ] Pose fold tree FOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.651818 seconds to load from binary\nprotocols.loops.loops_main: Added cutpoint variant to residue 75\nprotocols.loops.loops_main: Added cutpoint variant to residue 76\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1201 rotamers at 44 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 649.218 649.218\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 1 649.218\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 585.944 585.944\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.737 583.737\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.328 583.328\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.519 583.328\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.189 583.189\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.669 582.669\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 583.527 582.669\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.69 582.669\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.412 582.412\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 582.412 582.412\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.663 581.663\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.111 581.111\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 581.071 581.071\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.612 580.612\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 8/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.696 580.612\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 580.19 580.19\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 9/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.842 579.842\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.628 579.628\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 1/5 10/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.232 579.232\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.633 579.232\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 1088 rotamers at 43 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.633 579.232\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: cycle: 2 579.69\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 1/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.585 579.585\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.512 579.512\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 2/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.98 579.512\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.247 579.247\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 3/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.1 579.1\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.161 579.1\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 4/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.127 579.1\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.158 579.1\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 5/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.183 579.1\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.833 578.833\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 6/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.978 578.833\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.109 578.833\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 2/5 7/10 \nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer.\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.144 578.833\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial.\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.task: Packer task: initialize from command line() \nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.95 578.833\nprotocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial.\nprotocols.loops.loop_mover.refine.LooKilled\n\nFinished T660_LoopBuilding in 0:17:04.052367", "state": "failed"}, "T700_FoldTree": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nFold tree --------------------------------------------------\nFOLD_TREE EDGE 1 116 -1 \nFOLD_TREE EDGE 1 30 -1 EDGE 30 40 -1 EDGE 30 50 1 EDGE 50 116 -1 EDGE 50 41 -1 \n116 5 1\nFOLD_TREE EDGE 1 30 -1 EDGE 30 40 -1 EDGE 30 50 1 EDGE 50 41 -1 EDGE 50 116 -1 \nFOLD_TREE \ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.38536 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n\nFinished T700_FoldTree in 0:00:47.120136", "state": "passed"}, "T800_ClassicRelax": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.46108 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nprotocols.relax.ClassicRelax: Setting up default relax setting\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.663767 seconds to load from binary\nprotocols.relax.ClassicRelax: \nprotocols.relax.ClassicRelax: \nprotocols.relax.ClassicRelax: ===================================================================\nprotocols.relax.ClassicRelax: Stage 1 Killed\n\nFinished T800_ClassicRelax in 0:17:04.038821", "state": "failed"}, "T850_SubClassing": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\nBase::Base()\nPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nA.__init__...\nPyValue.__init__...\nA.foo_int(1)\nA.foo_value(wrong...)\nA.foo_string(qwerty)\nNew Value[1]: A.foo_value! \n\nA.foo_value(wrong...)\nNew Value[2]: A.foo_value! \n\nA.foo_value_sp(wrong...)\nNew Value[3]: A.foo_value_sp! \n\nA.foo_int(1)\nA.foo_value(wrong...)\nA.foo_string(qwerty)\nNew Value[4]: A.foo_value! \n\nA.foo_int(1)\nA.foo_value(wrong...)\nA.foo_string(qwerty)\nNew Value[5]: A.foo_value! \n\nrosetta.utility.py.OverloadTest Test -----------------------\nOverloadTest::self_test_virtual_p...\n Calling test(Value *v)...\n Calling test(Value *v)... Done!\nOverloadTest::self_test_virtual_p... Done!\nOverloadTest::self_test_virtual_ref...\n Calling test(Value &v)...\n Calling test(Value &v)... Done!\nOverloadTest::self_test_virtual_ref... Done!\nPyOverloadTest Test -----------------------------------------\nOverloadTest::self_test_virtual_p...\n Calling test(Value *v)...\n Calling test(Value *v)... Done!\nOverloadTest::self_test_virtual_p... Done!\nOverloadTest::self_pure_test_virtual_p...\n Calling pure_test(Value *v)...\n Calling pure_test(Value *v)... Done!\nOverloadTest::self_pure_test_virtual_p... Done!\nOverloadTest::self_test_virtual_ref...\n Calling test(Value &v)...\n Calling test(Value &v)... Done!\nOverloadTest::self_test_virtual_ref... Done!\nOverloadTest::self_pure_test_virtual_ref...\n Calling pure_test(Value &v)...\n Calling pure_test(Value &v)... Done!\nOverloadTest::self_pure_test_virtual_ref... Done!\nPyOverloadTest.test_p(Value('unknown') )\nPyOverloadTest.pure_test_p(Value('unknown') )\nPyOverloadTest.test_ref(Value('unknown') )\nPyOverloadTest.pure_test_ref(Value('unknown') )\nMy_New_Mover.__init__...\nMy_New_Mover.apply: <class 'pyrosetta.rosetta.core.pose.Pose'>\nThis My_New_Mover apply...\nOld phi=0.0, new phi=1.54\nMyNewCI1B::__init__!\n---------------------------------------------\nScore: 232.0\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.42531 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\nValue destructor! [A.foo_value_sp!]\nValue destructor! [A.foo_value!]\nValue destructor! [unknown]\nValue destructor! [unknown]\n\nFinished T850_SubClassing in 0:00:47.237740", "state": "passed"}, "T860_SubClassing_EnergyMethods": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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---------------------------------------------\nMyCI1B_Method Score: 232.0\nprotocols.moves.MonteCarlo:\n\"Temperature\" (kT): 1\nTotal Trials: 0\nLowest Score: 232\nLast Accepted Score: 232\nlast_accept = 232\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.40545 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n\nFinished T860_SubClassing_EnergyMethods in 0:00:47.348961", "state": "passed"}, "T870_SubClassing_EnergyMethods2": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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---------------------------------------------\nCI1B_Method Score: 232.0\n---------------------------------------------\nCI2B_Method Score: 525.0\n---------------------------------------------\nCD2B_Method Score: 525.0\n\n\n\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.54456 seconds.\ncore.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB\n/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/test/T870_SubClassing_EnergyMethods2.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n from rosetta.core.scoring.methods import ContextIndependentOneBodyEnergy, ContextIndependentTwoBodyEnergy, ContextDependentTwoBodyEnergy\n\nFinished T870_SubClassing_EnergyMethods2 in 0:00:47.589416", "state": "passed"}, "T880_Other": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.42104 seconds.\ncore.import_pose.import_pose: File '../test/data/ligand_test.pdb' automatically determined to be of type PDB\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.659754 seconds to load from binary\ncore.import_pose.import_pose: File '../test/data/dna_test.pdb' automatically determined to be of type PDB\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name O5* to O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Converting atom name C5* to C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: Number of nucleic acid residue fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: -12 C DG GUA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: P \ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C5'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C4'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: C3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: missing: O3'\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 164 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 166 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 167 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 169 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 170 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 172 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 173 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 174 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:UpperRNA:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 175 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE:LowerDNA:VirtualDNAPhosphate\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 177 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file ../test/data/dna_test.pdb. Best match rsd_type: ADE\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 181 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 182 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 183 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 184 in file ../test/data/dna_test.pdb. Best match rsd_type: 5MU:deoxy_O2prime\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 185 in file ../test/data/dna_test.pdb. Best match rsd_type: GUA\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 186 in file ../test/data/dna_test.pdb. Best match rsd_type: CYT:UpperDNA\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for OP1 and OP2 for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue DT\ncore.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything.\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 161\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N9 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N7 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: C8 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue GUA:LowerDNA:VirtualDNAPhosphate 162\ncore.conformation.Conformation: Connecting residues: 162 ( GUA:LowerDNA:VirtualDNAPhosphate ) and 163 ( CYT ) at atoms O3' and P \ncore.conformation.Conformation: with mutual distances: 0.293633 and 0.00610344\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 163 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 164 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 165 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 166 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 167 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 168 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 169 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 170 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 171 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 172 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 173 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 174 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 175 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 176 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 177 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuildePyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\ntesting ligand modeling\ntesting DNA modeling\nDone!\nr: [ WARNING ] can't find pose atom for file-residue 178 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 179 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 181 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 182 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 183 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 184 atom 2H2' (trying to store temperature in PDBInfo)\ncore.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 185 atom 2H2' (trying to store temperature in PDBInfo)\ncore.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 12 atom name N9 \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\ncore.pack.pack_rotamers: built 1 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished T880_Other in 0:02:42.427330", "state": "passed"}, "T900_distributed": {"log": "Unsupported python version for pyrosetta.distributed: sys.version_info(major=3, minor=9, micro=14, releaselevel='final', serial=0)\n\nFinished T900_distributed in 0:00:00.324109", "state": "passed"}, "Workshop2test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.74929 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: 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/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/pyPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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: ../test/data/workshops/1YY8.clean.pdb\nTotal residues: 868\nSequence: DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS\nFold tree:\nFOLD_TREE EDGE 1 213 -1 EDGE 1 214 1 EDGE 214 434 -1 EDGE 1 435 2 EDGE 435 647 -1 EDGE 1 648 3 EDGE 648 868 -1 \nDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS\nProtein has 868 residues.\nGLY\nC\n66\n100\n25 A \n1 9 17 25 33 41 49 57 65 73 \nDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVES\nLLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLH\n\n\n81 89 97 105 113 121 129 137 145 153 \nEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ\nHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLLEEEEEELLEELLLLEE\n\n\n161 169 177 185 193 201 209 217 225 233 \nESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGF\nEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEELLLLLLLEEEEEELLLLLEEEELLLEEELLLLLEEEEEEEELL\n\n\n241 249 257 265 273 281 289 297 305 313 \nSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFA\nLLLLLLEEEEEELLLLLEEEEEEELLLLLEEELHHHLLLEEEEEELLLLEEEEEELLLLHHHLEEEEEEEELLLLLLLEE\n\n\n321 329 337 345 353 361 369 377 385 393 \nYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV\nEELLLEEEEELLLLLELLEEEEELLLHHHEEHHEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEE\n\n\n401 409 417 425 433 441 449 457 465 473 \nVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSDILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRL\nEEEEHHHLLLLLLEEEEEEHHHLEEEEEELLLLLLLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEE\n\n\n481 489 497 505 513 521 529 537 545 553 \nLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLK\nEEELLLEELLLLLLLEEEEEELLEEEEEELLLLHHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHH\n\n\n561 569 577 585 593 601 609 617 625 633 \nSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVT\nHLEEEEEEEEEEEELLLEEEEEEELLEEELLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEEELLLLLLEE\n\n\n641 649 657 665 673 681 689 697 705 713 \nKSFNRGAQVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDN\nEEEELLLLLEEEELLLEEELLLLLEEEEEEEELLLLLLLLEEEEEELLLLLEEEEEEELLLLLEEELHHHLLLEEEEEEL\n\n\n721 729 737 745 753 761 769 777 785 793 \nSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP\nLLLEEEEEELLLLHHHLEEEEEEEELLLLLLLEEEELLLEEEEELLLLLELLEEEEELLLHHHEEHHEEEEEEEEEEEEL\n\n\n801 809 817 825 833 841 849 857 865 \nEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS\nLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHHHLLLLEEEEEEHHHLEEEEEELLLLL\n\n\n-112.78988533697459\n119.19490144825458\n-59.969147488992036\n1.4632323807242649\n1.5092534578393384\n<bound method PyCapsule.norm of <pyrosetta.rosetta.numeric.xyzVector_double_t object at 0x4027d94c70>>\n1.887434528690777\nthon-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.707746 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished Workshop2test in 0:02:58.834117", "state": "passed"}, "Workshop3test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.48121 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/6Q21.clean.pdb' automatically determined to be of type PDB\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.647793 seconds to load from binary\ncore.scoring.ScoreFunction: \n------------------------------------------------------------\n Scores Weight Raw Score Wghtd.Score\n------------------------------------------------------------\n fa_atr 1.000 -4241.897 -4241.897\n fa_rep 0.550 4336.454 2385.050\n fa_sol 1.000 2798.424 2798.424\n fa_intra_rep 0.005 3035.687 15.178\n fa_intra_sol_xover4 1.000 180.944 180.944\n lk_ball_wtd 1.000 -56.460 -56.460\n fa_elec 1.000 -933.702 -933.702\n pro_close 1.250 270.565 338.206\n hbond_sr_bb 1.000 -181.224 -181.224\n hbond_lr_bb 1.000 -130.586 -130.586\n hbond_bb_sc 1.000 -58.168 -58.168\n hbond_sc 1.000 -38.850 -38.850\n dslf_fa13 1.250 0.000 0.000\n omega 0.400 149.145 59.658\n fa_dun 0.700 4635.733 3245.013\n p_aa_pp 0.600 -101.427 -60.856\n yhh_planarity 0.625 0.000 0.000\n ref 1.000 188.455 188.455\n rama_prepro 0.450 591.830 266.324\n---------------------------------------------------\n Total weighted score: 3775.512\ncore.scoring.Energies: E fa_atr fa_rep fa_sol fa_intra_repfa_intra_sol_x lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref rama_prepro\ncore.scoring.Energies: E(i) 24 -7.40 19.03 2.94 8.76 0.09 -0.11 -0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.12 2.68 0.06 0.00 2.30 3.58\ncore.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 162 GLU OE1 1.87 152.3 115.2 157.1 1.000 -1.850\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 165 GLN OE1 1.59 159.1 136.2 147.7 0.859 -1.567\ncore.scoring.hbonds.HBondSet: #A 52 LEU N A 2 THR O 1.59 171.0 149.6 134.7 1.000 -0.439\ncore.scoring.hbonds.HBondSet: #A 2 THR N A 50 THR O 2.01 158.3 155.0 -175.7 1.000 -1.342\ncore.scoring.hbonds.HBondSet: #A 4 TYR N A 52 LEU O 1.71 146.0 157.4 151.1 1.000 -0.468\ncore.scoring.hbonds.HBondSet: #A 54 ASP N A 4 TYR O 1.72 151.1 150.2 49.0 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #A 5 LYS N A 76 GLU OE1 1.52 175.1 149.4 13.9 0.765 -1.324\ncore.scoring.hbonds.HBondSet: #A 76 GLU N A 5 LYS O 1.97 142.0 123.6 -73.8 1.000 -0.616\ncore.scoring.hbonds.HBondSet: #A 77 GLY N A 5 LYS O 2.16 141.0 146.4 -155.0 1.000 -0.989\ncore.scoring.hbonds.HBondSet: #A 6 LEU N A 54 ASP O 1.88 169.2 151.8 102.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #A 56 LEU N A 6 LEU O 2.05 163.6 163.5 167.1 1.000 -1.200\ncore.scoring.hbonds.HBondSet: #A 7 VAL N A 77 GLY O 1.65 159.9 148.6 -140.0 1.000 -0.669\ncore.scoring.hbonds.HBondSet: #A 8 VAL N A 56 LEU O 2.14 166.5 145.2 73.7 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 8 VAL O 2.66 140.8 137.3 32.0 1.000 -0.139\ncore.scoring.hbonds.HBondSet: #A 81 VAL N A 9 VAL O 1.76 166.8 144.1 -124.3 1.000 -0.996\ncore.scoring.hbonds.HBondSet: #A 9 VAL N A 79 LEU O 1.98 138.4 151.4 57.5 1.000 -0.592\ncore.scoring.hbonds.HBondSet: #A 14 VAL N A 11 ALA O 1.88 154.8 146.6 -154.7 1.000 -1.324\ncore.scoring.hbonds.HBondSet: #A 117 LYS NZ A 13 GLY O 2.09 158.9 168.0 43.3 0.929 -0.307\ncore.scoring.hbonds.HBondSet: #A 116 ASN ND2A 14 VAL O 2.17 167.3 134.9 147.9 1.000 -1.433\ncore.scoring.hbonds.HBondSet: #A 19 LEU N A 15 GLY O 1.86 152.2 155.7 -122.2 1.000 -0.811\ncore.scoring.hbonds.HBondSet: #A 20 THR N A 16 LYS O 1.90 177.7 161.6 -167.9 1.000 -1.327\ncore.scoring.hbonds.HBondSet: #A 21 ILE N A 17 SER O 1.81 151.9 161.2 83.6 1.000 -0.613\ncore.scoring.hbonds.HBondSet: #A 17 SER OG A 57 ASP OD2 1.82 126.8 115.0 -166.4 1.000 -0.827\ncore.scoring.hbonds.HBondSet: #A 22 GLN N A 18 ALA O 2.31 140.8 122.1 -104.6 1.000 -0.323\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 19 LEU O 2.28 137.6 137.1 -174.9 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 20 THR O 1.97 123.1 112.5 -78.8 1.000 -0.055\ncore.scoring.hbonds.HBondSet: #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979\ncore.scoring.hbonds.HBondSet: #A 25 GLN N A 21 ILE O 2.24 105.4 127.6 -17.1 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 22 GLN O 1.69 156.8 124.3 126.5 0.859 -0.895\ncore.scoring.hbonds.HBondSet: #A 30 ASP N A 31 GLU OE2 1.95 148.8 110.5 52.5 0.318 -1.124\ncore.scoring.hbonds.HBondSet: #A 57 ASP N A 38 ASP O 2.02 149.5 176.9 -58.1 1.000 -0.727\ncore.scoring.hbonds.HBondSet: #A 40 TYR N A 55 ILE O 2.06 133.0 125.1 62.1 1.000 -0.543\ncore.scoring.hbonds.HBondSet: #A 55 ILE N A 40 TYR O 1.69 157.5 167.5 -58.5 1.000 -0.451\ncore.scoring.hbonds.HBondSet: #A 42 LYS N A 53 LEU O 2.02 144.4 129.4 31.9 1.000 -1.371\ncore.scoring.hbonds.HBondSet: #A 53 LEU N A 42 LYS O 1.74 153.8 165.7 -34.7 1.000 -0.598\ncore.scoring.hbonds.HBondSet: #A 43 GLN NE2B 141 TYR O 1.70 166.6 150.3 33.2 0.859 -1.175\ncore.scoring.hbonds.HBondSet: #B 141 TYR N A 43 GLN OE1 2.24 131.2 99.3 -167.7 0.859 -0.219\ncore.scoring.hbonds.HBondSet: #A 44 VAL N A 51 CYS O 1.71 163.4 149.6 -1.3 1.000 -1.165\ncore.scoring.hbonds.HBondSet: #A 46 ILE N A 49 GLU O 2.07 141.6 134.8 -34.7 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #A 49 GLU N A 46 ILE O 2.22 146.3 99.6 95.0 1.000 -0.222\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD1 2.30 127.4 91.6 172.3 0.718 -0.063\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD2 2.37 163.9 86.4 -172.5 0.718 -0.412\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH1A 47 ASP OD2 1.48 142.3 122.9 -33.8 0.671 -0.468\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH2A 47 ASP OD2 1.87 128.8 120.1 73.7 0.671 -0.154\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH1A 49 GLU OE2 1.85 136.1 126.0 132.0 0.624 -0.645\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH2A 49 GLU OE2 2.28 126.2 161.1 -104.1 0.624 -0.007\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 56 LEU O 2.50 117.5 111.9 -148.7 1.000 -0.051\ncore.scoring.hbonds.HBondSet: #A 65 SER N A 63 GLU OE1 1.63 154.5 118.5 115.9 0.224 -0.884\ncore.scoring.hbonds.HBondSet: #A 68 ARG NH2A 96 TYR OH 1.81 164.5 113.9 -150.2 0.788 -1.692\ncore.scoring.hbonds.HBondSet: #A 74 THR OG1A 71 TYR O 2.00 159.3 114.5 -39.3 0.576 -0.378\ncore.scoring.hbonds.HBondSet: #A 71 TYR N A 72 MET O 2.18 108.7 111.7 7.3 1.000 -0.617\ncore.scoring.hbonds.HBondSet: #A 75 GLY N A 71 TYR O 1.64 137.5 150.1 -159.0 1.000 -0.191\ncore.scoring.hbonds.HBondSet: #A 104 LYS NZ A 75 GLY O 1.73 151.1 175.2 27.0 0.788 -0.427\ncore.scoring.hbonds.HBondSet: #A 112 VAL N A 78 PHE O 2.25 148.8 157.4 173.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 78 PHE N A 110 PRO O 2.01 158.7 153.2 -144.4 1.000 -1.242\ncore.scoring.hbonds.HBondSet: #A 80 CYS N A 112 VAL O 2.27 143.1 149.0 68.7 1.000 -0.434\ncore.scoring.hbonds.HBondSet: #A 114 VAL N A 80 CYS O 2.23 169.9 156.5 101.6 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 116 ASN N A 82 PHE O 1.76 152.5 166.5 -98.5 1.000 -0.518\ncore.scoring.hbonds.HBondSet: #A 82 PHE N A 114 VAL O 2.14 145.0 155.1 -96.1 1.000 -0.561\ncore.scoring.hbonds.HBondSet: #A 86 ASN N A 83 ALA O 2.32 149.5 107.5 -109.9 1.000 -0.454\ncore.scoring.hbonds.HBondSet: #A 83 ALA N A 89 SER OG 1.92 159.9 113.0 146.0 1.000 -2.159\ncore.scoring.hbonds.HBondSet: #A 84 ILE N A 116 ASN O 2.25 158.9 161.3 -45.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 124 THR N A 84 ILE O 1.65 177.5 159.1 166.1 1.000 -0.788\ncore.scoring.hbonds.HBondSet: #A 88 LYS N A 86 ASN OD1 1.96 146.5 130.0 -97.6 0.600 -0.800\ncore.scoring.hbonds.HBondSet: #A 90 PHE N A 86 ASN O 2.39 155.4 153.6 -141.6 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #A 91 GLU N A 87 THR O 2.43 136.5 134.7 -143.4 1.000 -0.557\ncore.scoring.hbonds.HBondSet: #A 92 ASP N A 88 LYS O 2.28 145.5 141.1 -118.0 1.000 -0.589\ncore.scoring.hbonds.HBondSet: #A 96 TYR N A 92 ASP O 2.47 148.2 144.3 139.2 1.000 -0.571\ncore.scoring.hbonds.HBondSet: #A 95 GLN N A 92 ASP O 1.65 147.8 124.5 -102.5 1.000 -0.067\ncore.scoring.hbonds.HBondSet: #A 97 ARG N A 93 ILE O 2.13 156.0 164.2 -73.0 1.000 -0.838\ncore.scoring.hbonds.HBondSet: #A 98 GLU N A 94 HIS O 2.17 155.1 127.3 -111.1 1.000 -0.919\ncore.scoring.hbonds.HBondSet: #A 99 GLN N A 95 GLN O 2.20 147.3 151.5 -140.0 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #A 100 ILE N A 96 TYR O 2.07 160.1 159.6 177.7 1.000 -1.238\ncore.scoring.hbonds.HBondSet: #A 101 LYS N A 97 ARG O 2.17 173.1 164.2 -178.2 1.000 -1.217\ncore.scoring.hbonds.HBondSet: #A 102 ARG N A 98 GLU O 2.38 139.0 138.2 -136.4 1.000 -0.549\ncore.scoring.hbonds.HBondSet: #A 103 VAL N A 99 GLN O 1.71 166.8 162.3 -144.5 1.000 -0.762\ncore.scoring.hbonds.HBondSet: #A 104 LYS N A 100 ILE O 1.67 160.9 170.6 -154.6 1.000 -0.436\ncore.scoring.hbonds.HBondSet: #A 105 ASP N A 102 ARG O 2.25 143.4 93.6 -86.8 1.000 -0.002\ncore.scoring.hbonds.HBondSet: #A 108 ASP N A 106 SER OG 1.97 152.0 90.6 86.3 0.365 -1.113\ncore.scoring.hbonds.HBondSet: #A 113 LEU N A 140 PRO O 1.81 148.3 171.8 67.9 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #A 142 ILE N A 113 LEU O 1.79 150.9 160.0 151.3 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #A 115 GLY N A 142 ILE O 2.24 157.4 135.9 129.0 1.000 -1.120\ncore.scoring.hbonds.HBondSet: #A 144 THR N A 115 GLY O 2.13 162.0 119.4 101.2 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 116 ASN OD1 1.85 141.7 101.3 -66.8 1.000 -0.539\ncore.scoring.hbonds.HBondSet: #A 120 LEU N A 117 LYS O 1.95 172.9 143.4 -107.1 1.000 -1.171\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 144 THR O 2.01 106.8 129.9 -132.7 1.000 -0.125\ncore.scoring.hbonds.HBondSet: #A 118 CYS N A 144 THR O 1.90 170.5 123.4 123.6 1.000 -1.398\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 143 GLU OE2 1.95 158.1 107.0 -145.0 0.741 -1.215\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH2A 143 GLU OE1 1.63 171.8 119.9 158.6 0.741 -1.303\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 125 VAL O 2.02 173.1 148.1 -124.0 0.694 -1.007\ncore.scoring.hbonds.HBondSet: #A 130 ALA N A 126 GLU O 1.87 158.8 152.0 -177.9 1.000 -1.364\ncore.scoring.hbonds.HBondSet: #A 132 ASP N A 128 ARG O 2.21 150.7 138.4 -109.6 1.000 -0.724\ncore.scoring.hbonds.HBondSet: #A 133 LEU N A 129 GLN O 2.28 151.1 146.3 -142.0 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 134 ALA N A 130 ALA O 1.79 166.2 162.7 -178.5 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #A 135 ARG N A 131 GLN O 1.83 166.3 155.5 -99.9 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #A 136 SER N A 132 ASP O 1.78 156.7 145.2 -115.7 1.000 -0.779\ncore.scoring.hbonds.HBondSet: #A 137 TYR N A 133 LEU O 1.92 158.6 154.8 -155.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #A 138 GLY N A 134 ALA O 1.83 121.8 139.0 -163.6 1.000 -0.700\ncore.scoring.hbonds.HBondSet: #A 139 ILE N A 134 ALA O 2.24 163.7 126.8 83.5 1.000 -0.871\ncore.scoring.hbonds.HBondSet: #A 141 TYR OH A 143 GLU OE2 1.54 139.3 111.7 0.2 0.953 -1.165\ncore.scoring.hbonds.HBondSet: #A 141 TYR N C 43 GLN OE1 2.08 161.9 118.7 -172.1 0.835 -2.242\ncore.scoring.hbonds.HBondSet: #C 43 GLN NE2A 141 TYR O 2.33 146.4 124.9 79.1 0.835 -0.190\ncore.scoring.hbonds.HBondSet: #A 148 THR N A 145 SER OG 2.05 157.6 137.3 -91.6 0.694 -1.629\ncore.scoring.hbonds.HBondSet: #A 145 SER N A 150 GLN O 2.02 170.9 150.4 -53.6 1.000 -1.299\ncore.scoring.hbonds.HBondSet: #A 150 GLN N A 148 THR OG1 2.60 158.2 106.0 37.4 0.553 -0.009\ncore.scoring.hbonds.HBondSet: #A 152 VAL N A 149 ARG O 2.41 170.1 119.9 -103.6 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 153 GLU OE2 2.57 140.9 135.9 23.0 0.671 -0.460\ncore.scoring.hbonds.HBondSet: #A 155 ALA N A 151 GLY O 2.17 152.2 149.8 -130.5 1.000 -0.948\ncore.scoring.hbonds.HBondSet: #A 156 PHE N A 152 VAL O 2.47 167.0 144.2 -123.9 1.000 -0.728\ncore.scoring.hbonds.HBondSet: #A 157 TYR N A 153 GLU O 1.72 169.3 166.5 -179.4 1.000 -0.834\ncore.scoring.hbonds.HBondSet: #A 157 TYR OH A 153 GLU OE1 2.17 146.9 99.0 117.3 0.765 -0.012\ncore.scoring.hbonds.HBondSet: #A 158 THR N A 154 ASP O 1.89 147.3 139.5 -98.2 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #A 159 LEU N A 155 ALA O 2.17 148.5 137.9 -132.2 1.000 -1.027\ncore.scoring.hbonds.HBondSet: #A 160 VAL N A 156 PHE O 2.05 159.9 143.0 -132.0 1.000 -1.295\ncore.scoring.hbonds.HBondSet: #A 161 ARG N A 157 TYR O 1.81 160.4 153.3 -118.9 1.000 -0.892\ncore.scoring.hbonds.HBondSet: #A 162 GLU N A 158 THR O 2.08 152.2 148.4 -125.7 1.000 -0.984\ncore.scoring.hbonds.HBondSet: #A 163 ILE N A 159 LEU O 2.04 159.2 154.3 -135.6 1.000 -1.160\ncore.scoring.hbonds.HBondSet: #A 164 ARG N A 160 VAL O 1.82 170.5 164.7 -100.1 1.000 -0.943\ncore.scoring.hbonds.HBondSet: #A 165 GLN N A 161 ARG O 1.77 162.3 145.7 -126.0 1.000 -0.962\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 162 GLU OE2 1.52 173.9 111.2 -150.8 0.859 -1.532\ncore.scoring.hbonds.HBondSet: #A 166 HIS N A 162 GLU O 1.67 153.5 143.8 -117.4 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #A 167 LYS N A 163 ILE O 1.81 160.2 169.3 -164.8 1.000 -0.852\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 165 GLN OE1 1.68 168.3 116.6 -140.8 0.694 -1.841\ncore.scoring.hbonds.HBondSet: #A 168 LEU N A 165 GLN O 2.16 161.1 119.3 -109.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 167 LYS O 2.09 119.4 111.3 -127.2 1.000 -0.278\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 171 LEU O 2.31 134.6 103.8 72.2 1.000 -0.014\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 162 GLU OE2 1.78 162.3 101.4 -153.1 0.953 -1.514\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 165 GLN OE1 2.24 168.6 123.5 -111.6 0.741 -0.769\ncore.scoring.hbonds.HBondSet: #B 52 LEU N B 2 THR O 1.61 169.6 162.9 148.4 1.000 -0.412\ncore.scoring.hbonds.HBondSet: #B 2 THR N B 50 THR O 2.03 162.9 155.5 -160.6 1.000 -1.366\ncore.scoring.hbonds.HBondSet: #B 4 TYR N B 52 LEU O 1.80 164.8 167.3 95.8 1.000 -0.828\ncore.scoring.hbonds.HBondSet: #B 54 ASP N B 4 TYR O 1.94 154.4 155.9 57.8 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #B 4 TYR OH B 49 GLU OE1 1.84 151.6 105.5 143.8 0.812 -0.974\ncore.scoring.hbonds.HBondSet: #B 5 LYS N B 76 GLU OE1 1.53 174.9 152.7 -34.8 0.765 -1.099\ncore.scoring.hbonds.HBondSet: #B 76 GLU N B 5 LYS O 1.69 161.1 146.8 -26.4 1.000 -1.018\ncore.scoring.hbonds.HBondSet: #B 77 GLY N B 5 LYS O 2.40 143.5 155.6 146.2 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #B 6 LEU N B 54 ASP O 2.00 144.1 139.4 96.3 1.000 -0.600\ncore.scoring.hbonds.HBondSet: #B 56 LEU N B 6 LEU O 1.66 162.8 157.9 174.1 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #B 79 LEU N B 7 VAL O 1.74 157.3 152.8 147.5 1.000 -0.891\ncore.scoring.hbonds.HBondSet: #B 7 VAL N B 77 GLY O 2.02 174.4 161.6 166.4 1.000 -1.357\ncore.scoring.hbonds.HBondSet: #B 58 THR N B 8 VAL O 2.72 146.2 149.3 -11.1 1.000 -0.011\ncore.scoring.hbonds.HBondSet: #B 8 VAL N B 56 LEU O 1.97 177.7 162.1 69.5 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 9 VAL N B 79 LEU O 1.99 152.6 143.2 57.5 1.000 -1.020\ncore.scoring.hbonds.HBondSet: #B 81 VAL N B 9 VAL O 1.91 177.5 153.5 -123.6 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #B 14 VAL N B 11 ALA O 2.39 160.5 137.3 -127.2 1.000 -0.898\ncore.scoring.hbonds.HBondSet: #B 19 LEU N B 15 GLY O 1.91 147.7 148.4 -139.0 1.000 -0.998\ncore.scoring.hbonds.HBondSet: #B 20 THR N B 16 LYS O 1.82 178.0 165.1 -147.9 1.000 -1.102\ncore.scoring.hbonds.HBondSet: #B 21 ILE N B 17 SER O 1.94 143.6 134.8 -118.0 1.000 -0.775\ncore.scoring.hbonds.HBondSet: #B 17 SER OG B 57 ASP OD2 2.05 111.8 116.7 177.1 1.000 -0.366\ncore.scoring.hbonds.HBondSet: #B 22 GLN N B 18 ALA O 1.97 153.3 145.9 -100.8 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #B 23 LEU N B 19 LEU O 2.30 169.7 154.3 -159.7 1.000 -1.230\ncore.scoring.hbonds.HBondSet: #B 24 ILE N B 20 THR O 2.14 171.9 143.2 -132.6 1.000 -1.403\ncore.scoring.hbonds.HBondSet: #B 25 GLN N B 21 ILE O 1.99 147.2 133.1 -81.7 1.000 -0.687\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 21 ILE O 2.58 123.3 138.4 -158.7 1.000 -0.044\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 22 GLN O 1.79 133.6 118.3 -62.9 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #B 38 ASP N B 57 ASP O 1.85 160.4 146.8 -3.4 1.000 -1.515\ncore.scoring.hbonds.HBondSet: #B 57 ASP N B 38 ASP O 1.89 149.2 160.7 -105.2 1.000 -0.676\ncore.scoring.hbonds.HBondSet: #B 40 TYR N B 55 ILE O 2.11 143.2 150.5 52.1 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #B 55 ILE N B 40 TYR O 2.12 137.4 137.0 -91.8 1.000 -0.380\ncore.scoring.hbonds.HBondSet: #B 42 LYS N B 53 LEU O 1.91 134.3 138.2 49.9 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #B 44 VAL N B 51 CYS O 1.91 173.0 163.2 -19.0 1.000 -1.262\ncore.scoring.hbonds.HBondSet: #B 51 CYS N B 44 VAL O 1.70 159.6 163.0 112.3 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #B 46 ILE N B 49 GLU O 1.89 149.1 141.5 15.9 1.000 -1.413\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 46 ILE O 1.91 143.8 123.3 -75.0 0.835 -0.513\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD2 2.06 128.7 100.1 -167.7 0.718 -0.614\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD1 1.97 118.9 114.3 145.6 0.718 -0.498\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH1B 47 ASP OD2 1.52 144.2 128.2 -31.0 0.741 -0.595\ncore.scoring.hbonds.HBondSet: #B 164 ARG NE B 49 GLU OE1 2.22 142.9 142.9 -117.5 0.788 -0.542\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 49 GLU OE1 2.04 151.6 123.3 -27.3 0.788 -1.398\ncore.scoring.hbonds.HBondSet: #B 63 GLU N B 62 GLU OE2 2.31 142.0 107.1 -34.1 0.341 -0.378\ncore.scoring.hbonds.HBondSet: #B 68 ARG N B 64 TYR O 2.21 159.0 142.6 -170.1 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #B 66 ALA N B 68 ARG O 2.47 136.1 106.6 33.2 1.000 -0.418\ncore.scoring.hbonds.HBondSet: #B 69 ASP N B 67 MET O 1.74 106.9 117.0 -154.2 1.000 -0.195\ncore.scoring.hbonds.HBondSet: #B 70 GLN N B 67 MET O 1.98 119.6 120.4 -45.6 1.000 -0.524\ncore.scoring.hbonds.HBondSet: #B 71 TYR N B 67 MET O 2.16 162.9 149.0 67.5 1.000 -1.022\ncore.scoring.hbonds.HBondSet: #B 73 ARG N B 69 ASP O 2.51 126.5 117.9 -129.1 1.000 -0.007\ncore.scoring.hbonds.HBondSet: #B 73 ARG NH2B 69 ASP OD1 2.57 139.8 133.2 -39.3 0.459 -0.260\ncore.scoring.hbonds.HBondSet: #B 74 THR N B 70 GLN O 2.49 146.7 125.7 -106.1 1.000 -0.149\ncore.scoring.hbonds.HBondSet: #B 75 GLY N B 71 TYR O 1.87 145.5 145.5 -114.3 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #B 112 VAL N B 78 PHE O 2.16 146.2 176.3 179.0 1.000 -0.584\ncore.scoring.hbonds.HBondSet: #B 78 PHE N B 110 PRO O 2.04 158.2 134.9 -140.7 1.000 -1.502\ncore.scoring.hbonds.HBondSet: #B 114 VAL N B 80 CYS O 1.97 165.7 143.0 81.3 1.000 -1.057\ncore.scoring.hbonds.HBondSet: #B 80 CYS N B 112 VAL O 1.96 160.5 171.4 -82.6 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 116 ASN N B 82 PHE O 2.01 161.1 144.6 -120.6 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 86 ASN N B 83 ALA O 1.81 161.3 117.4 -107.2 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #B 83 ALA N B 89 SER OG 1.96 171.4 124.8 149.0 1.000 -2.326\ncore.scoring.hbonds.HBondSet: #B 84 ILE N B 116 ASN O 1.99 170.8 165.9 28.4 1.000 -1.215\ncore.scoring.hbonds.HBondSet: #B 124 THR N B 84 ILE O 2.25 143.4 147.0 -164.4 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 89 SER N B 86 ASN OD1 1.35 169.0 136.5 -89.4 0.929 -0.473\ncore.scoring.hbonds.HBondSet: #B 90 PHE N B 86 ASN O 2.39 149.6 128.9 -139.9 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 87 THR OG1B 124 THR OG1 1.94 120.7 134.4 95.7 0.576 -0.105\ncore.scoring.hbonds.HBondSet: #B 91 GLU N B 87 THR O 1.86 159.4 146.8 -126.5 1.000 -1.080\ncore.scoring.hbonds.HBondSet: #B 92 ASP N B 88 LYS O 2.02 132.2 148.3 -133.4 1.000 -0.579\ncore.scoring.hbonds.HBondSet: #B 96 TYR N B 92 ASP O 2.17 155.0 146.9 149.5 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #B 97 ARG N B 93 ILE O 2.00 161.9 151.3 -100.5 1.000 -1.005\ncore.scoring.hbonds.HBondSet: #B 98 GLU N B 94 HIS O 2.09 144.5 133.0 -121.8 1.000 -0.859\ncore.scoring.hbonds.HBondSet: #B 99 GLN N B 95 GLN O 1.75 174.2 171.9 -172.4 1.000 -0.848\ncore.scoring.hbonds.HBondSet: #B 100 ILE N B 96 TYR O 1.99 154.7 141.5 -129.9 1.000 -1.183\ncore.scoring.hbonds.HBondSet: #B 97 ARG NH1B 98 GLU OE1 2.08 102.1 136.3 167.3 0.600 -0.281\ncore.scoring.hbonds.HBondSet: #B 101 LYS N B 97 ARG O 2.20 169.3 146.3 -103.0 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 102 ARG N B 98 GLU O 2.10 155.0 157.1 -125.1 1.000 -0.944\ncore.scoring.hbonds.HBondSet: #B 103 VAL N B 99 GLN O 2.07 144.8 153.9 -148.4 1.000 -0.924\ncore.scoring.hbonds.HBondSet: #B 104 LYS N B 101 LYS O 2.32 156.3 98.4 -104.6 1.000 -0.333\ncore.scoring.hbonds.HBondSet: #B 105 ASP N B 101 LYS O 1.87 114.7 134.2 -113.9 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 106 SER N B 104 LYS O 2.12 146.8 90.6 135.1 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #B 142 ILE N B 113 LEU O 2.29 151.5 148.5 168.3 1.000 -1.122\ncore.scoring.hbonds.HBondSet: #B 113 LEU N B 140 PRO O 2.26 166.9 142.6 -106.9 1.000 -0.939\ncore.scoring.hbonds.HBondSet: #B 115 GLY N B 142 ILE O 1.89 175.4 163.3 115.9 1.000 -1.115\ncore.scoring.hbonds.HBondSet: #B 144 THR N B 115 GLY O 1.82 166.4 143.8 108.2 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #B 116 ASN ND2B 144 THR OG1 2.11 151.9 114.3 74.4 1.000 -1.625\ncore.scoring.hbonds.HBondSet: #B 120 LEU N B 117 LYS O 1.61 160.9 146.4 -148.9 1.000 -0.638\ncore.scoring.hbonds.HBondSet: #B 118 CYS N B 144 THR O 2.26 149.6 158.9 128.3 1.000 -0.664\ncore.scoring.hbonds.HBondSet: #B 122 ALA N B 120 LEU O 2.39 118.6 115.2 -135.1 1.000 -0.091\ncore.scoring.hbonds.HBondSet: #B 123 ARG NE B 125 VAL O 1.27 158.8 151.8 151.1 0.859 -0.468\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH1B 143 GLU OE1 2.43 152.6 131.2 154.5 0.835 -1.002\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH2B 143 GLU OE2 2.05 144.9 97.4 -150.9 0.835 -0.765\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 126 GLU O 2.05 144.5 148.6 -178.6 1.000 -1.206\ncore.scoring.hbonds.HBondSet: #B 126 GLU N B 129 GLN OE1 1.82 136.4 92.4 58.0 0.482 -0.121\ncore.scoring.hbonds.HBondSet: #B 129 GLN N B 126 GLU O 2.06 119.8 113.4 -80.2 1.000 -0.010\ncore.scoring.hbonds.HBondSet: #B 128 ARG NH2B 127 SER OG 1.74 118.8 110.7 98.3 0.435 -0.082\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 127 SER O 1.83 123.3 115.7 -86.8 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 131 GLN N B 127 SER O 1.62 168.0 152.9 134.3 1.000 -0.522\ncore.scoring.hbonds.HBondSet: #B 132 ASP N B 128 ARG O 1.71 157.8 144.0 -118.8 1.000 -0.662\ncore.scoring.hbonds.HBondSet: #B 133 LEU N B 129 GLN O 2.33 152.8 121.1 -102.2 1.000 -0.556\ncore.scoring.hbonds.HBondSet: #B 134 ALA N B 130 ALA O 1.84 166.9 159.5 -175.0 1.000 -1.226\ncore.scoring.hbonds.HBondSet: #B 135 ARG N B 131 GLN O 1.92 146.8 146.1 -91.4 1.000 -0.623\ncore.scoring.hbonds.HBondSet: #B 136 SER N B 132 ASP O 2.11 155.5 152.5 -172.9 1.000 -1.320\ncore.scoring.hbonds.HBondSet: #B 137 TYR N B 133 LEU O 2.17 133.9 144.9 -123.0 1.000 -0.463\ncore.scoring.hbonds.HBondSet: #B 138 GLY N B 134 ALA O 1.85 135.9 139.4 -133.7 1.000 -0.690\ncore.scoring.hbonds.HBondSet: #B 139 ILE N B 134 ALA O 1.78 172.1 146.2 58.4 1.000 -1.059\ncore.scoring.hbonds.HBondSet: #B 141 TYR OH B 143 GLU OE2 1.30 169.7 124.0 -22.7 0.953 -1.194\ncore.scoring.hbonds.HBondSet: #B 149 ARG N B 145 SER O 1.85 110.9 146.3 -130.1 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 148 THR N B 145 SER OG 2.10 165.0 108.1 -79.1 0.694 -2.084\ncore.scoring.hbonds.HBondSet: #B 145 SER N B 150 GLN O 1.80 163.2 158.2 -5.1 1.000 -1.148\ncore.scoring.hbonds.HBondSet: #B 150 GLN N B 148 THR OG1 2.31 163.9 114.4 48.9 0.576 -1.417\ncore.scoring.hbonds.HBondSet: #B 152 VAL N B 149 ARG O 2.57 162.8 114.6 -116.9 1.000 -0.414\ncore.scoring.hbonds.HBondSet: #B 155 ALA N B 151 GLY O 1.98 152.5 142.8 -118.1 1.000 -0.965\ncore.scoring.hbonds.HBondSet: #B 156 PHE N B 152 VAL O 2.52 168.0 149.9 -128.4 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #B 157 TYR N B 153 GLU O 2.01 159.5 148.4 -101.6 1.000 -0.968\ncore.scoring.hbonds.HBondSet: #B 158 THR N B 154 ASP O 1.96 151.7 136.5 -81.7 1.000 -0.789\ncore.scoring.hbonds.HBondSet: #B 159 LEU N B 155 ALA O 2.49 137.7 130.1 -132.6 1.000 -0.327\ncore.scoring.hbonds.HBondSet: #B 160 VAL N B 156 PHE O 2.28 136.6 138.3 -137.9 1.000 -0.671\ncore.scoring.hbonds.HBondSet: #B 161 ARG N B 157 TYR O 2.05 160.9 147.4 -145.4 1.000 -1.405\ncore.scoring.hbonds.HBondSet: #B 162 GLU N B 158 THR O 1.98 142.2 135.1 -129.6 1.000 -0.935\ncore.scoring.hbonds.HBondSet: #B 163 ILE N B 159 LEU O 2.27 145.9 130.6 -115.9 1.000 -0.628\ncore.scoring.hbonds.HBondSet: #B 164 ARG N B 160 VAL O 1.87 170.6 168.8 -122.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #B 165 GLN N B 161 ARG O 1.97 158.8 148.5 -96.5 1.000 -0.933\ncore.scoring.hbonds.HBondSet: #B 166 HIS N B 162 GLU O 2.15 141.4 126.0 -121.4 1.000 -0.756\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 163 ILE O 2.28 116.2 139.1 -144.3 1.000 -0.241\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 164 ARG O 2.22 148.2 99.2 -95.0 1.000 -0.254\ncore.scoring.hbonds.HBondSet: #B 168 LEU N B 165 GLN O 2.06 156.0 105.9 -96.2 1.000 -0.731\ncore.scoring.hbonds.HBondSet: #B 165 GLN NE2B 169 ARG O 2.02 154.2 163.2 -90.6 0.600 -0.731\ncore.scoring.hbonds.HBondSet: #C 2 THR N C 50 THR O 1.72 154.1 148.6 160.0 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 52 LEU N C 2 THR O 1.55 161.2 156.3 126.4 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #C 4 TYR OH C 49 GLU OE1 1.43 137.8 91.5 160.8 0.859 -0.322\ncore.scoring.hbonds.HBondSet: #C 4 TYR N C 52 LEU O 2.12 158.0 146.8 110.8 1.000 -0.956\ncore.scoring.hbonds.HBondSet: #C 54 ASP N C 4 TYR O 2.02 153.2 152.3 86.2 1.000 -0.814\ncore.scoring.hbonds.HBondSet: #C 5 LYS N C 76 GLU OE1 1.63 176.7 141.4 -69.2 0.718 -1.026\ncore.scoring.hbonds.HBondSet: #C 76 GLU N C 5 LYS O 1.69 153.2 142.2 -29.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #C 77 GLY N C 5 LYS O 2.17 159.7 146.5 136.1 1.000 -1.218\ncore.scoring.hbonds.HBondSet: #C 6 LEU N C 54 ASP O 2.32 137.6 138.1 85.2 1.000 -0.152\ncore.scoring.hbonds.HBondSet: #C 56 LEU N C 6 LEU O 1.75 173.5 163.1 -159.7 1.000 -0.981\ncore.scoring.hbonds.HBondSet: #C 7 VAL N C 77 GLY O 2.04 157.7 156.7 -176.3 1.000 -1.280\ncore.scoring.hbonds.HBondSet: #C 79 LEU N C 7 VAL O 2.04 161.1 151.4 106.5 1.000 -1.011\ncore.scoring.hbonds.HBondSet: #C 8 VAL N C 56 LEU O 1.70 168.1 175.5 -29.1 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #C 58 THR N C 8 VAL O 2.51 149.3 152.2 -34.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #C 81 VAL N C 9 VAL O 1.97 169.4 138.7 -95.1 1.000 -1.087\ncore.scoring.hbonds.HBondSet: #C 9 VAL N C 79 LEU O 1.99 163.0 158.5 69.8 1.000 -1.041\ncore.scoring.hbonds.HBondSet: #C 14 VAL N C 11 ALA O 2.53 152.2 138.8 -142.7 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #C 116 ASN ND2C 14 VAL O 1.82 167.4 146.4 -179.9 1.000 -1.537\ncore.scoring.hbonds.HBondSet: #C 20 THR N C 16 LYS O 1.99 167.4 144.5 -123.1 1.000 -1.282\ncore.scoring.hbonds.HBondSet: #C 21 ILE N C 17 SER O 1.82 165.5 158.8 -113.3 1.000 -0.929\ncore.scoring.hbonds.HBondSet: #C 22 GLN N C 18 ALA O 2.38 136.0 129.7 -113.7 1.000 -0.171\ncore.scoring.hbonds.HBondSet: #C 23 LEU N C 19 LEU O 2.36 161.8 147.0 -120.0 1.000 -0.796\ncore.scoring.hbonds.HBondSet: #C 24 ILE N C 20 THR O 2.00 166.6 151.1 -111.1 1.000 -1.125\ncore.scoring.hbonds.HBondSet: #C 25 GLN N C 21 ILE O 1.72 154.7 129.3 -67.1 1.000 -0.607\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 21 ILE O 2.57 119.1 135.6 -156.2 1.000 -0.015\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 22 GLN O 1.79 133.4 103.5 -60.3 1.000 -0.147\ncore.scoring.hbonds.HBondSet: #C 22 GLN NE2C 146 ALA O 1.63 154.0 167.5 -163.7 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #C 149 ARG NE C 22 GLN O 2.21 140.1 113.0 69.0 0.812 -0.272\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 22 GLN O 1.88 151.2 126.3 147.7 0.812 -1.210\ncore.scoring.hbonds.HBondSet: #C 42 LYS NZ C 23 LEU O 1.67 132.9 144.5 165.1 0.812 -0.372\ncore.scoring.hbonds.HBondSet: #C 27 HIS NE2C 25 GLN OE1 1.52 162.8 154.3 6.2 0.435 -1.662\ncore.scoring.hbonds.HBondSet: #C 38 ASP N C 57 ASP O 2.03 155.3 145.6 -28.1 1.000 -1.404\ncore.scoring.hbonds.HBondSet: #C 57 ASP N C 38 ASP O 1.79 175.4 159.9 -62.4 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #C 41 ARG NE C 40 TYR O 1.84 155.4 116.2 116.0 0.671 -0.817\ncore.scoring.hbonds.HBondSet: #C 40 TYR N C 55 ILE O 2.07 139.9 138.2 60.9 1.000 -0.682\ncore.scoring.hbonds.HBondSet: #C 55 ILE N C 40 TYR O 2.01 140.2 128.7 -92.3 1.000 -0.492\ncore.scoring.hbonds.HBondSet: #C 42 LYS N C 53 LEU O 1.92 154.7 134.6 29.2 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #C 53 LEU N C 42 LYS O 1.68 151.6 151.7 111.2 1.000 -0.308\ncore.scoring.hbonds.HBondSet: #C 44 VAL N C 51 CYS O 1.85 164.6 152.3 -11.9 1.000 -1.400\ncore.scoring.hbonds.HBondSet: #C 51 CYS N C 44 VAL O 1.80 154.4 157.7 -123.0 1.000 -0.742\ncore.scoring.hbonds.HBondSet: #C 46 ILE N C 49 GLU O 1.67 145.0 151.1 -29.9 1.000 -0.420\ncore.scoring.hbonds.HBondSet: #C 161 ARG NE C 47 ASP OD2 1.79 167.7 111.2 -154.9 0.741 -1.399\ncore.scoring.hbonds.HBondSet: #C 161 ARG NH2C 47 ASP OD1 1.31 152.2 114.3 134.3 0.741 -0.155\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH1C 47 ASP OD2 1.79 144.3 119.0 -34.0 0.694 -1.005\ncore.scoring.hbonds.HBondSet: #C 164 ARG NE C 49 GLU OE1 2.09 148.3 123.1 -106.5 0.765 -0.680\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH2C 49 GLU OE1 1.98 150.7 130.9 -21.0 0.765 -1.389\ncore.scoring.hbonds.HBondSet: #C 64 TYR N C 61 GLN O 2.09 163.3 134.6 -104.2 1.000 -1.046\ncore.scoring.hbonds.HBondSet: #C 67 MET N C 64 TYR O 2.24 163.1 120.2 -110.8 1.000 -0.992\ncore.scoring.hbonds.HBondSet: #C 68 ARG N C 65 SER O 2.45 162.1 114.3 -110.9 1.000 -0.588\ncore.scoring.hbonds.HBondSet: #C 71 TYR N C 67 MET O 2.78 160.9 130.8 -139.3 1.000 -0.124\ncore.scoring.hbonds.HBondSet: #C 72 MET N C 68 ARG O 1.90 156.3 161.6 -113.6 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 68 ARG NH1C 99 GLN OE1 2.34 152.0 138.5 126.6 0.718 -0.553\ncore.scoring.hbonds.HBondSet: #C 73 ARG N C 69 ASP O 2.24 126.8 126.8 -125.2 1.000 -0.354\ncore.scoring.hbonds.HBondSet: #C 74 THR N C 70 GLN O 2.31 145.5 139.3 -134.5 1.000 -0.795\ncore.scoring.hbonds.HBondSet: #C 75 GLY N C 71 TYR O 2.01 145.7 143.8 -113.0 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #C 78 PHE N C 110 PRO O 1.89 171.1 154.0 -133.0 1.000 -1.258\ncore.scoring.hbonds.HBondSet: #C 112 VAL N C 78 PHE O 2.26 137.9 153.6 -177.7 1.000 -0.706\ncore.scoring.hbonds.HBondSet: #C 114 VAL N C 80 CYS O 1.86 155.0 164.5 88.3 1.000 -0.760\ncore.scoring.hbonds.HBondSet: #C 80 CYS N C 112 VAL O 1.88 162.1 169.5 2.0 1.000 -1.001\ncore.scoring.hbonds.HBondSet: #C 82 PHE N C 114 VAL O 1.97 151.0 151.7 -114.5 1.000 -0.844\ncore.scoring.hbonds.HBondSet: #C 116 ASN N C 82 PHE O 1.73 153.8 170.9 -52.7 1.000 -0.479\ncore.scoring.hbonds.HBondSet: #C 86 ASN N C 83 ALA O 2.10 150.9 123.3 -107.8 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #C 83 ALA N C 89 SER OG 2.04 170.4 133.9 145.8 1.000 -2.012\ncore.scoring.hbonds.HBondSet: #C 84 ILE N C 116 ASN O 1.95 159.3 172.6 -73.4 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #C 124 THR N C 84 ILE O 1.76 153.0 166.8 -131.8 1.000 -0.587\ncore.scoring.hbonds.HBondSet: #C 125 VAL N C 84 ILE O 2.53 164.3 138.7 -65.9 1.000 -0.489\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN O 2.24 126.7 121.2 -94.4 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN OD1 2.15 151.2 132.2 -37.0 0.976 -1.308\ncore.scoring.hbonds.HBondSet: #C 90 PHE N C 86 ASN O 2.49 148.3 136.9 172.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #C 91 GLU N C 87 THR O 1.73 168.1 160.6 -136.9 1.000 -0.842\ncore.scoring.hbonds.HBondSet: #C 92 ASP N C 88 LYS O 1.77 142.1 145.1 -143.0 1.000 -0.721\ncore.scoring.hbonds.HBondSet: #C 93 ILE N C 89 SER O 2.27 134.8 151.0 -133.2 1.000 -0.401\ncore.scoring.hbonds.HBondSet: #C 95 GLN N C 92 ASP O 2.18 123.3 117.3 -80.6 1.000 -0.020\ncore.scoring.hbonds.HBondSet: #C 96 TYR N C 92 ASP O 2.15 160.9 154.3 168.7 1.000 -1.329\ncore.scoring.hbonds.HBondSet: #C 97 ARG N C 93 ILE O 1.67 175.6 168.1 -141.3 1.000 -0.605\ncore.scoring.hbonds.HBondSet: #C 98 GLU N C 94 HIS O 2.15 153.5 139.2 -126.1 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #C 99 GLN N C 95 GLN O 2.33 146.1 145.4 -117.0 1.000 -0.482\ncore.scoring.hbonds.HBondSet: #C 100 ILE N C 96 TYR O 2.09 167.1 158.5 -150.8 1.000 -1.289\ncore.scoring.hbonds.HBondSet: #C 101 LYS N C 97 ARG O 2.11 163.6 148.7 -126.8 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #C 102 ARG N C 98 GLU O 2.14 156.4 133.1 -120.4 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #C 103 VAL N C 99 GLN O 1.77 170.6 155.8 -107.8 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 104 LYS N C 100 ILE O 1.74 161.0 159.6 -109.4 1.000 -0.667\ncore.scoring.hbonds.HBondSet: #C 106 SER N C 101 LYS O 2.41 142.0 129.0 1.7 1.000 -1.169\ncore.scoring.hbonds.HBondSet: #C 102 ARG NH2C 105 ASP OD1 2.37 145.4 152.0 -158.6 0.318 -0.641\ncore.scoring.hbonds.HBondSet: #C 108 ASP N C 106 SER OG 2.22 135.0 142.4 -10.1 0.482 -0.020\ncore.scoring.hbonds.HBondSet: #C 169 ARG NH1C 108 ASP OD2 1.70 129.9 173.3 -0.5 0.412 -0.001\ncore.scoring.hbonds.HBondSet: #C 142 ILE N C 113 LEU O 1.88 166.1 166.9 171.9 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #C 113 LEU N C 140 PRO O 1.93 164.7 144.6 -108.0 1.000 -1.073\ncore.scoring.hbonds.HBondSet: #C 115 GLY N C 142 ILE O 2.04 164.1 154.8 175.7 1.000 -1.446\ncore.scoring.hbonds.HBondSet: #C 144 THR N C 115 GLY O 2.02 173.4 137.2 103.8 1.000 -1.173\ncore.scoring.hbonds.HBondSet: #C 120 LEU N C 117 LYS O 1.80 177.0 133.7 -108.6 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #C 118 CYS N C 144 THR O 1.85 163.3 151.8 126.7 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH1C 143 GLU OE1 2.17 169.7 110.4 151.0 0.765 -1.461\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 143 GLU OE2 1.91 161.0 121.8 -138.6 0.765 -1.288\ncore.scoring.hbonds.HBondSet: #C 123 ARG NE C 125 VAL O 2.03 131.2 124.9 118.0 0.718 -0.374\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 125 VAL O 1.68 140.4 134.2 -140.9 0.718 -0.735\ncore.scoring.hbonds.HBondSet: #C 130 ALA N C 126 GLU O 2.53 165.6 156.0 -159.6 1.000 -0.707\ncore.scoring.hbonds.HBondSet: #C 131 GLN N C 127 SER O 1.87 164.3 151.0 -110.2 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #C 132 ASP N C 128 ARG O 2.01 146.5 132.7 -107.0 1.000 -0.738\ncore.scoring.hbonds.HBondSet: #C 133 LEU N C 129 GLN O 1.98 143.1 129.4 -112.3 1.000 -0.717\ncore.scoring.hbonds.HBondSet: #C 134 ALA N C 130 ALA O 1.82 166.4 162.3 -156.9 1.000 -1.089\ncore.scoring.hbonds.HBondSet: #C 135 ARG N C 131 GLN O 2.10 173.9 148.9 -111.9 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #C 135 ARG NH1C 132 ASP OD1 2.38 136.5 145.6 -62.9 0.647 -0.181\ncore.scoring.hbonds.HBondSet: #C 136 SER N C 132 ASP O 2.12 152.8 137.7 -125.8 1.000 -1.072\ncore.scoring.hbonds.HBondSet: #C 137 TYR N C 133 LEU O 1.85 167.1 151.6 -134.6 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #C 139 ILE N C 134 ALA O 1.96 155.3 118.9 78.3 1.000 -0.895\ncore.scoring.hbonds.HBondSet: #C 141 TYR N D 43 GLN OE1 2.04 144.7 105.1 -161.4 0.882 -1.464\ncore.scoring.hbonds.HBondSet: #D 43 GLN NE2C 141 TYR O 2.03 157.6 130.4 65.6 0.882 -0.956\ncore.scoring.hbonds.HBondSet: #C 141 TYR OH C 143 GLU OE2 1.55 152.8 103.6 -1.4 0.929 -1.224\ncore.scoring.hbonds.HBondSet: #C 148 THR N C 145 SER OG 2.52 155.7 104.8 -76.2 0.718 -0.373\ncore.scoring.hbonds.HBondSet: #C 145 SER N C 150 GLN O 2.05 141.0 168.7 41.9 1.000 -0.559\ncore.scoring.hbonds.HBondSet: #C 152 VAL N C 149 ARG O 2.51 168.9 127.3 -107.7 1.000 -0.552\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH1C 153 GLU OE2 1.56 159.7 126.3 71.8 0.600 -0.384\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 153 GLU OE2 2.54 125.7 139.4 -17.5 0.600 -0.123\ncore.scoring.hbonds.HBondSet: #C 155 ALA N C 151 GLY O 1.78 146.1 133.1 -129.0 1.000 -0.800\ncore.scoring.hbonds.HBondSet: #C 156 PHE N C 152 VAL O 1.89 154.0 157.7 -140.7 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 157 TYR N C 153 GLU O 1.84 163.0 153.4 -86.5 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #C 158 THR N C 154 ASP O 1.94 154.1 142.2 -89.4 1.000 -0.813\ncore.scoring.hbonds.HBondSet: #C 159 LEU N C 155 ALA O 2.54 144.2 134.9 -128.1 1.000 -0.262\ncore.scoring.hbonds.HBondSet: #C 160 VAL N C 156 PHE O 2.21 149.1 137.4 -143.0 1.000 -1.172\ncore.scoring.hbonds.HBondSet: #C 161 ARG N C 157 TYR O 1.89 162.8 155.6 -160.3 1.000 -1.302\ncore.scoring.hbonds.HBondSet: #C 162 GLU N C 158 THR O 1.95 165.7 151.2 -131.2 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #C 163 ILE N C 159 LEU O 2.23 149.1 141.0 -119.3 1.000 -0.761\ncore.scoring.hbonds.HBondSet: #C 164 ARG N C 160 VAL O 1.88 171.9 160.2 -115.2 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 165 GLN N C 161 ARG O 1.82 176.3 172.4 -139.7 1.000 -0.999\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 162 GLU OE1 1.82 144.1 91.7 156.6 0.976 -0.691\ncore.scoring.hbonds.HBondSet: #C 166 HIS N C 162 GLU O 1.92 156.4 138.7 -120.0 1.000 -1.074\ncore.scoring.hbonds.HBondSet: #C 167 LYS N C 163 ILE O 2.12 124.3 130.8 -138.7 1.000 -0.641\ncore.scoring.hbonds.HBondSet: #C 168 LEU N C 164 ARG O 1.86 161.1 155.6 -106.6 1.000 -0.912\ncore.scoring.hbonds.HBondSet: #C 169 ARG N C 165 GLN O 2.29 139.6 150.6 -146.4 1.000 -0.622\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 165 GLN OE1 2.12 146.2 99.8 128.5 0.835 -0.554\ncore.scoring.hbonds.HBondSet: #C 171 LEU N C 168 LEU O 1.81 154.8 164.8 -70.6 1.000 -0.694\ncore.scoring.hbonds.HBondSet: #C 170 LYS NZ C 169 ARG O 1.86 133.9 108.9 117.0 0.224 -0.059\ncore.scoring.hbonds.HBondSet: #D 2 THR N D 50 THR O 1.98 153.0 167.9 155.1 1.000 -0.894\ncore.scoring.hbonds.HBondSet: #D 52 LEU N D 2 THR O 1.72 167.6 145.5 124.6 1.000 -0.897\ncore.scoring.hbonds.HBondSet: #D 4 TYR OH D 49 GLU OE1 1.87 148.2 90.6 -158.3 0.882 -0.520\ncore.scoring.hbonds.HBondSet: #D 4 TYR N D 52 LEU O 1.66 165.8 167.6 97.1 1.000 -0.435\ncore.scoring.hbonds.HBondSet: #D 54 ASP N D 4 TYR O 1.72 166.4 154.7 93.8 1.000 -0.648\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 4 TYR OH 2.59 162.8 134.0 74.5 0.882 -0.402\ncore.scoring.hbonds.HBondSet: #D 77 GLY N D 5 LYS O 2.52 134.7 154.4 -178.2 1.000 -0.113\ncore.scoring.hbonds.HBondSet: #D 5 LYS N D 76 GLU OE1 1.54 165.0 142.6 22.7 0.765 -1.391\ncore.scoring.hbonds.HBondSet: #D 76 GLU N D 5 LYS O 1.91 160.2 145.4 -56.2 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 56 LEU N D 6 LEU O 1.72 178.1 168.9 -117.8 1.000 -0.751\ncore.scoring.hbonds.HBondSet: #D 6 LEU N D 54 ASP O 1.90 160.8 152.3 94.5 1.000 -0.918\ncore.scoring.hbonds.HBondSet: #D 7 VAL N D 77 GLY O 2.11 157.8 159.9 -165.5 1.000 -1.145\ncore.scoring.hbonds.HBondSet: #D 79 LEU N D 7 VAL O 1.88 166.4 146.8 124.1 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #D 8 VAL N D 56 LEU O 1.77 169.6 175.1 81.8 1.000 -0.833\ncore.scoring.hbonds.HBondSet: #D 58 THR N D 8 VAL O 2.43 152.2 149.9 16.5 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #D 81 VAL N D 9 VAL O 1.75 169.0 165.2 144.8 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #D 9 VAL N D 79 LEU O 1.93 170.0 167.2 70.2 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #D 14 VAL N D 11 ALA O 2.38 148.7 141.4 -128.6 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #D 116 ASN ND2D 14 VAL O 1.67 147.0 135.1 141.6 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 19 LEU N D 15 GLY O 2.05 151.7 143.9 -99.6 1.000 -0.793\ncore.scoring.hbonds.HBondSet: #D 20 THR N D 16 LYS O 2.13 166.6 143.6 -107.4 1.000 -1.071\ncore.scoring.hbonds.HBondSet: #D 17 SER OG D 57 ASP OD2 1.87 114.6 107.7 -177.0 1.000 -0.488\ncore.scoring.hbonds.HBondSet: #D 21 ILE N D 17 SER O 1.79 154.9 149.8 -137.3 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 22 GLN N D 18 ALA O 1.86 153.5 140.6 -123.6 1.000 -0.977\ncore.scoring.hbonds.HBondSet: #D 23 LEU N D 19 LEU O 2.14 158.4 150.3 -145.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #D 24 ILE N D 20 THR O 2.07 155.1 140.7 -108.5 1.000 -0.925\ncore.scoring.hbonds.HBondSet: #D 25 GLN N D 21 ILE O 1.56 132.7 142.6 -9.3 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #D 26 ASN N D 21 ILE O 2.41 136.2 146.1 167.6 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #D 149 ARG NE D 22 GLN O 2.12 139.8 117.6 63.3 0.835 -0.464\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 22 GLN O 2.01 139.9 146.0 137.3 0.835 -0.652\ncore.scoring.hbonds.HBondSet: #D 29 VAL N D 27 HIS O 2.47 111.1 116.9 -152.8 1.000 -0.086\ncore.scoring.hbonds.HBondSet: #D 59 ALA N D 37 GLU OE1 2.23 169.0 99.2 -26.6 0.647 -0.979\ncore.scoring.hbonds.HBondSet: #D 57 ASP N D 38 ASP O 2.02 159.9 148.4 112.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 40 TYR N D 55 ILE O 1.66 150.7 149.5 -0.6 1.000 -0.730\ncore.scoring.hbonds.HBondSet: #D 55 ILE N D 40 TYR O 1.94 155.8 135.9 -80.6 1.000 -0.876\ncore.scoring.hbonds.HBondSet: #D 41 ARG NH2D 54 ASP OD1 2.11 156.8 122.7 133.7 0.647 -1.186\ncore.scoring.hbonds.HBondSet: #D 42 LYS N D 53 LEU O 2.24 133.2 129.7 31.0 1.000 -0.930\ncore.scoring.hbonds.HBondSet: #D 53 LEU N D 42 LYS O 1.82 169.1 144.4 75.9 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #D 42 LYS NZ D 157 TYR OH 2.05 139.6 157.2 168.5 0.812 -0.099\ncore.scoring.hbonds.HBondSet: #D 44 VAL N D 51 CYS O 1.90 142.6 139.5 2.6 1.000 -1.373\ncore.scoring.hbonds.HBondSet: #D 51 CYS N D 44 VAL O 1.71 161.1 161.3 18.3 1.000 -0.780\ncore.scoring.hbonds.HBondSet: #D 46 ILE N D 49 GLU O 1.90 136.6 145.3 -57.8 1.000 -0.553\ncore.scoring.hbonds.HBondSet: #D 49 GLU N D 46 ILE O 2.00 157.3 116.2 99.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 46 ILE O 2.07 136.9 109.4 -56.9 0.765 -0.451\ncore.scoring.hbonds.HBondSet: #D 161 ARG NE D 47 ASP OD2 1.82 167.5 111.8 -159.4 0.718 -1.487\ncore.scoring.hbonds.HBondSet: #D 161 ARG NH2D 47 ASP OD1 1.72 157.2 113.8 147.4 0.718 -1.127\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH1D 47 ASP OD2 2.23 122.1 98.1 -39.4 0.647 -0.042\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 49 GLU OE1 2.08 121.5 136.8 -92.4 0.765 -0.014\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 49 GLU OE1 1.40 140.1 138.2 49.8 0.765 -0.005\ncore.scoring.hbonds.HBondSet: #D 70 GLN N D 67 MET O 2.17 136.5 115.0 -98.6 1.000 -0.317\ncore.scoring.hbonds.HBondSet: #D 72 MET N D 68 ARG O 1.99 166.7 160.7 -170.5 1.000 -1.316\ncore.scoring.hbonds.HBondSet: #D 102 ARG NH1D 69 ASP OD2 2.19 136.9 124.8 139.4 0.459 -0.823\ncore.scoring.hbonds.HBondSet: #D 73 ARG N D 69 ASP O 1.97 140.8 139.1 -103.9 1.000 -0.550\ncore.scoring.hbonds.HBondSet: #D 74 THR N D 70 GLN O 2.16 137.2 131.6 -177.7 1.000 -1.376\ncore.scoring.hbonds.HBondSet: #D 75 GLY N D 72 MET O 2.38 158.1 105.7 -99.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #D 78 PHE N D 110 PRO O 2.05 157.7 144.7 -143.1 1.000 -1.368\ncore.scoring.hbonds.HBondSet: #D 112 VAL N D 78 PHE O 2.10 143.2 152.5 -172.7 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 114 VAL N D 80 CYS O 1.72 164.9 149.5 117.5 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 80 CYS N D 112 VAL O 1.95 161.0 172.9 34.9 1.000 -0.982\ncore.scoring.hbonds.HBondSet: #D 82 PHE N D 114 VAL O 2.03 167.4 170.3 75.0 1.000 -1.069\ncore.scoring.hbonds.HBondSet: #D 116 ASN N D 82 PHE O 2.12 146.4 173.7 -3.8 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #D 86 ASN N D 83 ALA O 2.54 144.5 114.1 -111.9 1.000 -0.035\ncore.scoring.hbonds.HBondSet: #D 83 ALA N D 89 SER OG 2.11 146.5 117.3 152.5 0.976 -1.646\ncore.scoring.hbonds.HBondSet: #D 124 THR N D 84 ILE O 1.93 160.3 139.9 136.2 1.000 -1.379\ncore.scoring.hbonds.HBondSet: #D 125 VAL N D 84 ILE O 2.05 139.0 162.4 -12.1 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #D 84 ILE N D 116 ASN O 1.94 147.6 177.3 -97.9 1.000 -0.661\ncore.scoring.hbonds.HBondSet: #D 89 SER N D 86 ASN OD1 2.00 161.6 108.1 -98.8 0.906 -0.997\ncore.scoring.hbonds.HBondSet: #D 90 PHE N D 86 ASN O 2.32 158.0 145.2 -158.1 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #D 91 GLU N D 87 THR O 1.78 158.6 144.7 -139.2 1.000 -1.110\ncore.scoring.hbonds.HBondSet: #D 88 LYS NZ D 91 GLU OE1 2.12 150.6 156.0 -89.7 0.459 -0.167\ncore.scoring.hbonds.HBondSet: #D 92 ASP N D 88 LYS O 1.73 149.1 145.6 -122.1 1.000 -0.547\ncore.scoring.hbonds.HBondSet: #D 93 ILE N D 90 PHE O 2.03 147.4 105.4 -96.7 1.000 -0.527\ncore.scoring.hbonds.HBondSet: #D 94 HIS N D 91 GLU O 2.28 154.2 119.5 -110.3 1.000 -0.747\ncore.scoring.hbonds.HBondSet: #D 95 GLN N D 92 ASP O 1.97 143.9 112.2 -97.6 1.000 -0.551\ncore.scoring.hbonds.HBondSet: #D 96 TYR N D 92 ASP O 2.30 161.1 156.2 175.1 1.000 -1.118\ncore.scoring.hbonds.HBondSet: #D 97 ARG N D 93 ILE O 2.05 176.1 164.5 -98.8 1.000 -1.133\ncore.scoring.hbonds.HBondSet: #D 98 GLU N D 94 HIS O 2.48 142.6 122.3 -120.3 1.000 -0.261\ncore.scoring.hbonds.HBondSet: #D 99 GLN N D 95 GLN O 1.99 161.3 153.0 -125.4 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 100 ILE N D 96 TYR O 1.87 177.4 169.1 -152.0 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #D 101 LYS N D 97 ARG O 1.86 167.3 142.3 -115.0 1.000 -1.108\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 98 GLU O 2.22 125.0 130.7 -126.1 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 99 GLN O 2.09 133.2 99.1 -93.1 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #D 103 VAL N D 99 GLN O 1.88 169.2 172.6 -128.9 1.000 -1.037\ncore.scoring.hbonds.HBondSet: #D 104 LYS N D 100 ILE O 1.81 170.9 160.9 -48.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 106 SER N D 101 LYS O 2.55 140.0 125.9 -41.0 1.000 -0.377\ncore.scoring.hbonds.HBondSet: #D 108 ASP N D 106 SER OG 2.21 137.3 143.4 13.5 0.459 -0.092\ncore.scoring.hbonds.HBondSet: #D 142 ILE N D 113 LEU O 2.18 165.5 165.0 143.8 1.000 -1.054\ncore.scoring.hbonds.HBondSet: #D 113 LEU N D 140 PRO O 1.99 168.8 165.8 -121.5 1.000 -1.121\ncore.scoring.hbonds.HBondSet: #D 144 THR N D 115 GLY O 2.05 151.3 119.0 102.4 1.000 -0.815\ncore.scoring.hbonds.HBondSet: #D 115 GLY N D 142 ILE O 2.14 152.6 145.4 126.2 1.000 -0.985\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 116 ASN OD1 1.95 135.6 102.0 -56.4 1.000 -0.502\ncore.scoring.hbonds.HBondSet: #D 146 ALA N D 116 ASN OD1 2.50 148.1 139.3 174.2 1.000 -0.040\ncore.scoring.hbonds.HBondSet: #D 120 LEU N D 117 LYS O 1.73 153.1 140.1 -82.7 1.000 -0.460\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 144 THR O 2.23 116.8 127.4 -123.2 1.000 -0.076\ncore.scoring.hbonds.HBondSet: #D 118 CYS N D 144 THR O 1.88 157.5 150.5 118.9 1.000 -0.964\ncore.scoring.hbonds.HBondSet: #D 123 ARG NE D 125 VAL O 1.82 128.0 130.3 143.5 0.624 -0.648\ncore.scoring.hbonds.HBondSet: #D 130 ALA N D 126 GLU O 2.57 166.7 149.2 -153.7 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 128 ARG NH2D 127 SER OG 2.10 123.3 96.6 53.1 0.412 -0.055\ncore.scoring.hbonds.HBondSet: #D 131 GLN N D 127 SER O 1.81 150.8 149.5 -138.0 1.000 -0.911\ncore.scoring.hbonds.HBondSet: #D 132 ASP N D 128 ARG O 1.96 143.7 138.7 -118.4 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #D 133 LEU N D 129 GLN O 2.05 154.0 149.6 -123.9 1.000 -1.006\ncore.scoring.hbonds.HBondSet: #D 134 ALA N D 130 ALA O 2.04 172.6 153.4 -117.2 1.000 -1.210\ncore.scoring.hbonds.HBondSet: #D 135 ARG N D 131 GLN O 2.00 157.8 139.8 -105.8 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 136 SER N D 132 ASP O 1.90 143.1 135.1 -132.5 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 137 TYR N D 133 LEU O 1.93 138.5 144.3 -145.7 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 134 ALA O 2.06 114.7 140.4 -145.1 1.000 -0.403\ncore.scoring.hbonds.HBondSet: #D 139 ILE N D 134 ALA O 1.90 169.0 134.7 69.1 1.000 -1.158\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 135 ARG O 2.19 144.5 99.6 -80.6 1.000 -0.216\ncore.scoring.hbonds.HBondSet: #D 141 TYR OH D 143 GLU OE2 1.45 141.9 141.2 32.0 0.906 -0.834\ncore.scoring.hbonds.HBondSet: #D 148 THR N D 145 SER OG 2.21 162.4 109.0 -94.6 0.718 -1.869\ncore.scoring.hbonds.HBondSet: #D 145 SER N D 150 GLN O 2.05 157.8 160.0 -28.2 1.000 -1.124\ncore.scoring.hbonds.HBondSet: #D 149 ARG N D 145 SER O 2.27 108.0 131.2 -130.5 1.000 0.000\ncore.scoring.hbonds.HBondSet: #D 150 GLN N D 148 THR OG1 2.01 159.2 116.7 54.1 0.553 -1.978\ncore.scoring.hbonds.HBondSet: #D 152 VAL N D 149 ARG O 2.08 167.7 133.5 -113.0 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH1D 153 GLU OE2 1.72 139.9 116.1 110.6 0.624 -0.269\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 153 GLU OE2 2.14 128.3 171.8 -38.7 0.624 -0.141\ncore.scoring.hbonds.HBondSet: #D 155 ALA N D 151 GLY O 2.21 144.4 149.7 -122.7 1.000 -0.640\ncore.scoring.hbonds.HBondSet: #D 156 PHE N D 152 VAL O 2.49 164.9 140.1 -133.1 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #D 157 TYR N D 153 GLU O 1.61 176.4 168.7 -139.5 1.000 -0.343\ncore.scoring.hbonds.HBondSet: #D 159 LEU N D 155 ALA O 2.52 140.7 130.8 -124.7 1.000 -0.182\ncore.scoring.hbonds.HBondSet: #D 160 VAL N D 156 PHE O 2.09 159.7 161.6 -154.7 1.000 -1.128\ncore.scoring.hbonds.HBondSet: #D 161 ARG N D 157 TYR O 2.63 167.6 136.4 -88.2 1.000 -0.115\ncore.scoring.hbonds.HBondSet: #D 162 GLU N D 158 THR O 2.14 149.2 143.1 -142.7 1.000 -1.147\ncore.scoring.hbonds.HBondSet: #D 163 ILE N D 159 LEU O 1.94 160.5 153.2 -126.9 1.000 -1.117\ncore.scoring.hbonds.HBondSet: #D 164 ARG N D 160 VAL O 1.61 159.8 154.1 -143.4 1.000 -0.367\ncore.scoring.hbonds.HBondSet: #D 165 GLN N D 161 ARG O 1.72 164.1 141.9 -98.0 1.000 -0.642\ncore.scoring.hbonds.HBondSet: #D 166 HIS N D 162 GLU O 1.79 161.8 144.1 -107.5 1.000 -0.839\ncore.scoring.hbonds.HBondSet: #D 167 LYS N D 163 ILE O 1.99 160.5 154.2 -112.8 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 168 LEU N D 165 GLN O 2.12 141.5 110.2 -100.9 1.000 -0.446\ncore.scoring.hbonds.HBondSet: #D 169 ARG N D 166 HIS O 1.83 168.3 146.2 -120.5 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #D 170 LYS N D 167 LYS O 2.34 150.5 125.7 -124.0 1.000 -0.782\ncore.scoring.hbonds.HBondSet: #Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 162 GLU OE1 1.87 152.3 115.2 157.1 1.000 -1.850\ncore.scoring.hbonds.HBondSet: #A 1 MET N B 165 GLN OE1 1.59 159.1 136.2 147.7 0.859 -1.567\ncore.scoring.hbonds.HBondSet: #A 52 LEU N A 2 THR O 1.59 171.0 149.6 134.7 1.000 -0.439\ncore.scoring.hbonds.HBondSet: #A 2 THR N A 50 THR O 2.01 158.3 155.0 -175.7 1.000 -1.342\ncore.scoring.hbonds.HBondSet: #A 4 TYR N A 52 LEU O 1.71 146.0 157.4 151.1 1.000 -0.468\ncore.scoring.hbonds.HBondSet: #A 54 ASP N A 4 TYR O 1.72 151.1 150.2 49.0 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #A 5 LYS N A 76 GLU OE1 1.52 175.1 149.4 13.9 0.765 -1.324\ncore.scoring.hbonds.HBondSet: #A 76 GLU N A 5 LYS O 1.97 142.0 123.6 -73.8 1.000 -0.616\ncore.scoring.hbonds.HBondSet: #A 77 GLY N A 5 LYS O 2.16 141.0 146.4 -155.0 1.000 -0.989\ncore.scoring.hbonds.HBondSet: #A 6 LEU N A 54 ASP O 1.88 169.2 151.8 102.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #A 56 LEU N A 6 LEU O 2.05 163.6 163.5 167.1 1.000 -1.200\ncore.scoring.hbonds.HBondSet: #A 7 VAL N A 77 GLY O 1.65 159.9 148.6 -140.0 1.000 -0.669\ncore.scoring.hbonds.HBondSet: #A 8 VAL N A 56 LEU O 2.14 166.5 145.2 73.7 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 8 VAL O 2.66 140.8 137.3 32.0 1.000 -0.139\ncore.scoring.hbonds.HBondSet: #A 81 VAL N A 9 VAL O 1.76 166.8 144.1 -124.3 1.000 -0.996\ncore.scoring.hbonds.HBondSet: #A 9 VAL N A 79 LEU O 1.98 138.4 151.4 57.5 1.000 -0.592\ncore.scoring.hbonds.HBondSet: #A 14 VAL N A 11 ALA O 1.88 154.8 146.6 -154.7 1.000 -1.324\ncore.scoring.hbonds.HBondSet: #A 117 LYS NZ A 13 GLY O 2.09 158.9 168.0 43.3 0.929 -0.307\ncore.scoring.hbonds.HBondSet: #A 116 ASN ND2A 14 VAL O 2.17 167.3 134.9 147.9 1.000 -1.433\ncore.scoring.hbonds.HBondSet: #A 19 LEU N A 15 GLY O 1.86 152.2 155.7 -122.2 1.000 -0.811\ncore.scoring.hbonds.HBondSet: #A 20 THR N A 16 LYS O 1.90 177.7 161.6 -167.9 1.000 -1.327\ncore.scoring.hbonds.HBondSet: #A 21 ILE N A 17 SER O 1.81 151.9 161.2 83.6 1.000 -0.613\ncore.scoring.hbonds.HBondSet: #A 17 SER OG A 57 ASP OD2 1.82 126.8 115.0 -166.4 1.000 -0.827\ncore.scoring.hbonds.HBondSet: #A 22 GLN N A 18 ALA O 2.31 140.8 122.1 -104.6 1.000 -0.323\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 19 LEU O 2.28 137.6 137.1 -174.9 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #A 23 LEU N A 20 THR O 1.97 123.1 112.5 -78.8 1.000 -0.055\ncore.scoring.hbonds.HBondSet: #A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979\ncore.scoring.hbonds.HBondSet: #A 25 GLN N A 21 ILE O 2.24 105.4 127.6 -17.1 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 22 GLN O 1.69 156.8 124.3 126.5 0.859 -0.895\ncore.scoring.hbonds.HBondSet: #A 30 ASP N A 31 GLU OE2 1.95 148.8 110.5 52.5 0.318 -1.124\ncore.scoring.hbonds.HBondSet: #A 57 ASP N A 38 ASP O 2.02 149.5 176.9 -58.1 1.000 -0.727\ncore.scoring.hbonds.HBondSet: #A 40 TYR N A 55 ILE O 2.06 133.0 125.1 62.1 1.000 -0.543\ncore.scoring.hbonds.HBondSet: #A 55 ILE N A 40 TYR O 1.69 157.5 167.5 -58.5 1.000 -0.451\ncore.scoring.hbonds.HBondSet: #A 42 LYS N A 53 LEU O 2.02 144.4 129.4 31.9 1.000 -1.371\ncore.scoring.hbonds.HBondSet: #A 53 LEU N A 42 LYS O 1.74 153.8 165.7 -34.7 1.000 -0.598\ncore.scoring.hbonds.HBondSet: #A 43 GLN NE2B 141 TYR O 1.70 166.6 150.3 33.2 0.859 -1.175\ncore.scoring.hbonds.HBondSet: #B 141 TYR N A 43 GLN OE1 2.24 131.2 99.3 -167.7 0.859 -0.219\ncore.scoring.hbonds.HBondSet: #A 44 VAL N A 51 CYS O 1.71 163.4 149.6 -1.3 1.000 -1.165\ncore.scoring.hbonds.HBondSet: #A 46 ILE N A 49 GLU O 2.07 141.6 134.8 -34.7 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #A 49 GLU N A 46 ILE O 2.22 146.3 99.6 95.0 1.000 -0.222\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD1 2.30 127.4 91.6 172.3 0.718 -0.063\ncore.scoring.hbonds.HBondSet: #A 161 ARG NH1A 47 ASP OD2 2.37 163.9 86.4 -172.5 0.718 -0.412\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH1A 47 ASP OD2 1.48 142.3 122.9 -33.8 0.671 -0.468\ncore.scoring.hbonds.HBondSet: #A 164 ARG NH2A 47 ASP OD2 1.87 128.8 120.1 73.7 0.671 -0.154\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH1A 49 GLU OE2 1.85 136.1 126.0 132.0 0.624 -0.645\ncore.scoring.hbonds.HBondSet: #B 169 ARG NH2A 49 GLU OE2 2.28 126.2 161.1 -104.1 0.624 -0.007\ncore.scoring.hbonds.HBondSet: #A 58 THR N A 56 LEU O 2.50 117.5 111.9 -148.7 1.000 -0.051\ncore.scoring.hbonds.HBondSet: #A 65 SER N A 63 GLU OE1 1.63 154.5 118.5 115.9 0.224 -0.884\ncore.scoring.hbonds.HBondSet: #A 68 ARG NH2A 96 TYR OH 1.81 164.5 113.9 -150.2 0.788 -1.692\ncore.scoring.hbonds.HBondSet: #A 74 THR OG1A 71 TYR O 2.00 159.3 114.5 -39.3 0.576 -0.378\ncore.scoring.hbonds.HBondSet: #A 71 TYR N A 72 MET O 2.18 108.7 111.7 7.3 1.000 -0.617\ncore.scoring.hbonds.HBondSet: #A 75 GLY N A 71 TYR O 1.64 137.5 150.1 -159.0 1.000 -0.191\ncore.scoring.hbonds.HBondSet: #A 104 LYS NZ A 75 GLY O 1.73 151.1 175.2 27.0 0.788 -0.427\ncore.scoring.hbonds.HBondSet: #A 112 VAL N A 78 PHE O 2.25 148.8 157.4 173.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 78 PHE N A 110 PRO O 2.01 158.7 153.2 -144.4 1.000 -1.242\ncore.scoring.hbonds.HBondSet: #A 80 CYS N A 112 VAL O 2.27 143.1 149.0 68.7 1.000 -0.434\ncore.scoring.hbonds.HBondSet: #A 114 VAL N A 80 CYS O 2.23 169.9 156.5 101.6 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 116 ASN N A 82 PHE O 1.76 152.5 166.5 -98.5 1.000 -0.518\ncore.scoring.hbonds.HBondSet: #A 82 PHE N A 114 VAL O 2.14 145.0 155.1 -96.1 1.000 -0.561\ncore.scoring.hbonds.HBondSet: #A 86 ASN N A 83 ALA O 2.32 149.5 107.5 -109.9 1.000 -0.454\ncore.scoring.hbonds.HBondSet: #A 83 ALA N A 89 SER OG 1.92 159.9 113.0 146.0 1.000 -2.159\ncore.scoring.hbonds.HBondSet: #A 84 ILE N A 116 ASN O 2.25 158.9 161.3 -45.4 1.000 -0.878\ncore.scoring.hbonds.HBondSet: #A 124 THR N A 84 ILE O 1.65 177.5 159.1 166.1 1.000 -0.788\ncore.scoring.hbonds.HBondSet: #A 88 LYS N A 86 ASN OD1 1.96 146.5 130.0 -97.6 0.600 -0.800\ncore.scoring.hbonds.HBondSet: #A 90 PHE N A 86 ASN O 2.39 155.4 153.6 -141.6 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #A 91 GLU N A 87 THR O 2.43 136.5 134.7 -143.4 1.000 -0.557\ncore.scoring.hbonds.HBondSet: #A 92 ASP N A 88 LYS O 2.28 145.5 141.1 -118.0 1.000 -0.589\ncore.scoring.hbonds.HBondSet: #A 96 TYR N A 92 ASP O 2.47 148.2 144.3 139.2 1.000 -0.571\ncore.scoring.hbonds.HBondSet: #A 95 GLN N A 92 ASP O 1.65 147.8 124.5 -102.5 1.000 -0.067\ncore.scoring.hbonds.HBondSet: #A 97 ARG N A 93 ILE O 2.13 156.0 164.2 -73.0 1.000 -0.838\ncore.scoring.hbonds.HBondSet: #A 98 GLU N A 94 HIS O 2.17 155.1 127.3 -111.1 1.000 -0.919\ncore.scoring.hbonds.HBondSet: #A 99 GLN N A 95 GLN O 2.20 147.3 151.5 -140.0 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #A 100 ILE N A 96 TYR O 2.07 160.1 159.6 177.7 1.000 -1.238\ncore.scoring.hbonds.HBondSet: #A 101 LYS N A 97 ARG O 2.17 173.1 164.2 -178.2 1.000 -1.217\ncore.scoring.hbonds.HBondSet: #A 102 ARG N A 98 GLU O 2.38 139.0 138.2 -136.4 1.000 -0.549\ncore.scoring.hbonds.HBondSet: #A 103 VAL N A 99 GLN O 1.71 166.8 162.3 -144.5 1.000 -0.762\ncore.scoring.hbonds.HBondSet: #A 104 LYS N A 100 ILE O 1.67 160.9 170.6 -154.6 1.000 -0.436\ncore.scoring.hbonds.HBondSet: #A 105 ASP N A 102 ARG O 2.25 143.4 93.6 -86.8 1.000 -0.002\ncore.scoring.hbonds.HBondSet: #A 108 ASP N A 106 SER OG 1.97 152.0 90.6 86.3 0.365 -1.113\ncore.scoring.hbonds.HBondSet: #A 113 LEU N A 140 PRO O 1.81 148.3 171.8 67.9 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #A 142 ILE N A 113 LEU O 1.79 150.9 160.0 151.3 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #A 115 GLY N A 142 ILE O 2.24 157.4 135.9 129.0 1.000 -1.120\ncore.scoring.hbonds.HBondSet: #A 144 THR N A 115 GLY O 2.13 162.0 119.4 101.2 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 116 ASN OD1 1.85 141.7 101.3 -66.8 1.000 -0.539\ncore.scoring.hbonds.HBondSet: #A 120 LEU N A 117 LYS O 1.95 172.9 143.4 -107.1 1.000 -1.171\ncore.scoring.hbonds.HBondSet: #A 117 LYS N A 144 THR O 2.01 106.8 129.9 -132.7 1.000 -0.125\ncore.scoring.hbonds.HBondSet: #A 118 CYS N A 144 THR O 1.90 170.5 123.4 123.6 1.000 -1.398\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 143 GLU OE2 1.95 158.1 107.0 -145.0 0.741 -1.215\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH2A 143 GLU OE1 1.63 171.8 119.9 158.6 0.741 -1.303\ncore.scoring.hbonds.HBondSet: #A 123 ARG NH1A 125 VAL O 2.02 173.1 148.1 -124.0 0.694 -1.007\ncore.scoring.hbonds.HBondSet: #A 130 ALA N A 126 GLU O 1.87 158.8 152.0 -177.9 1.000 -1.364\ncore.scoring.hbonds.HBondSet: #A 132 ASP N A 128 ARG O 2.21 150.7 138.4 -109.6 1.000 -0.724\ncore.scoring.hbonds.HBondSet: #A 133 LEU N A 129 GLN O 2.28 151.1 146.3 -142.0 1.000 -0.960\ncore.scoring.hbonds.HBondSet: #A 134 ALA N A 130 ALA O 1.79 166.2 162.7 -178.5 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #A 135 ARG N A 131 GLN O 1.83 166.3 155.5 -99.9 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #A 136 SER N A 132 ASP O 1.78 156.7 145.2 -115.7 1.000 -0.779\ncore.scoring.hbonds.HBondSet: #A 137 TYR N A 133 LEU O 1.92 158.6 154.8 -155.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #A 138 GLY N A 134 ALA O 1.83 121.8 139.0 -163.6 1.000 -0.700\ncore.scoring.hbonds.HBondSet: #A 139 ILE N A 134 ALA O 2.24 163.7 126.8 83.5 1.000 -0.871\ncore.scoring.hbonds.HBondSet: #A 141 TYR OH A 143 GLU OE2 1.54 139.3 111.7 0.2 0.953 -1.165\ncore.scoring.hbonds.HBondSet: #A 141 TYR N C 43 GLN OE1 2.08 161.9 118.7 -172.1 0.835 -2.242\ncore.scoring.hbonds.HBondSet: #C 43 GLN NE2A 141 TYR O 2.33 146.4 124.9 79.1 0.835 -0.190\ncore.scoring.hbonds.HBondSet: #A 148 THR N A 145 SER OG 2.05 157.6 137.3 -91.6 0.694 -1.629\ncore.scoring.hbonds.HBondSet: #A 145 SER N A 150 GLN O 2.02 170.9 150.4 -53.6 1.000 -1.299\ncore.scoring.hbonds.HBondSet: #A 150 GLN N A 148 THR OG1 2.60 158.2 106.0 37.4 0.553 -0.009\ncore.scoring.hbonds.HBondSet: #A 152 VAL N A 149 ARG O 2.41 170.1 119.9 -103.6 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #A 149 ARG NH2A 153 GLU OE2 2.57 140.9 135.9 23.0 0.671 -0.460\ncore.scoring.hbonds.HBondSet: #A 155 ALA N A 151 GLY O 2.17 152.2 149.8 -130.5 1.000 -0.948\ncore.scoring.hbonds.HBondSet: #A 156 PHE N A 152 VAL O 2.47 167.0 144.2 -123.9 1.000 -0.728\ncore.scoring.hbonds.HBondSet: #A 157 TYR N A 153 GLU O 1.72 169.3 166.5 -179.4 1.000 -0.834\ncore.scoring.hbonds.HBondSet: #A 157 TYR OH A 153 GLU OE1 2.17 146.9 99.0 117.3 0.765 -0.012\ncore.scoring.hbonds.HBondSet: #A 158 THR N A 154 ASP O 1.89 147.3 139.5 -98.2 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #A 159 LEU N A 155 ALA O 2.17 148.5 137.9 -132.2 1.000 -1.027\ncore.scoring.hbonds.HBondSet: #A 160 VAL N A 156 PHE O 2.05 159.9 143.0 -132.0 1.000 -1.295\ncore.scoring.hbonds.HBondSet: #A 161 ARG N A 157 TYR O 1.81 160.4 153.3 -118.9 1.000 -0.892\ncore.scoring.hbonds.HBondSet: #A 162 GLU N A 158 THR O 2.08 152.2 148.4 -125.7 1.000 -0.984\ncore.scoring.hbonds.HBondSet: #A 163 ILE N A 159 LEU O 2.04 159.2 154.3 -135.6 1.000 -1.160\ncore.scoring.hbonds.HBondSet: #A 164 ARG N A 160 VAL O 1.82 170.5 164.7 -100.1 1.000 -0.943\ncore.scoring.hbonds.HBondSet: #A 165 GLN N A 161 ARG O 1.77 162.3 145.7 -126.0 1.000 -0.962\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 162 GLU OE2 1.52 173.9 111.2 -150.8 0.859 -1.532\ncore.scoring.hbonds.HBondSet: #A 166 HIS N A 162 GLU O 1.67 153.5 143.8 -117.4 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #A 167 LYS N A 163 ILE O 1.81 160.2 169.3 -164.8 1.000 -0.852\ncore.scoring.hbonds.HBondSet: #C 1 MET N A 165 GLN OE1 1.68 168.3 116.6 -140.8 0.694 -1.841\ncore.scoring.hbonds.HBondSet: #A 168 LEU N A 165 GLN O 2.16 161.1 119.3 -109.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 167 LYS O 2.09 119.4 111.3 -127.2 1.000 -0.278\ncore.scoring.hbonds.HBondSet: #A 169 ARG N A 171 LEU O 2.31 134.6 103.8 72.2 1.000 -0.014\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 162 GLU OE2 1.78 162.3 101.4 -153.1 0.953 -1.514\ncore.scoring.hbonds.HBondSet: #B 1 MET N D 165 GLN OE1 2.24 168.6 123.5 -111.6 0.741 -0.769\ncore.scoring.hbonds.HBondSet: #B 52 LEU N B 2 THR O 1.61 169.6 162.9 148.4 1.000 -0.412\ncore.scoring.hbonds.HBondSet: #B 2 THR N B 50 THR O 2.03 162.9 155.5 -160.6 1.000 -1.366\ncore.scoring.hbonds.HBondSet: #B 4 TYR N B 52 LEU O 1.80 164.8 167.3 95.8 1.000 -0.828\ncore.scoring.hbonds.HBondSet: #B 54 ASP N B 4 TYR O 1.94 154.4 155.9 57.8 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #B 4 TYR OH B 49 GLU OE1 1.84 151.6 105.5 143.8 0.812 -0.974\ncore.scoring.hbonds.HBondSet: #B 5 LYS N B 76 GLU OE1 1.53 174.9 152.7 -34.8 0.765 -1.099\ncore.scoring.hbonds.HBondSet: #B 76 GLU N B 5 LYS O 1.69 161.1 146.8 -26.4 1.000 -1.018\ncore.scoring.hbonds.HBondSet: #B 77 GLY N B 5 LYS O 2.40 143.5 155.6 146.2 1.000 -0.432\ncore.scoring.hbonds.HBondSet: #B 6 LEU N B 54 ASP O 2.00 144.1 139.4 96.3 1.000 -0.600\ncore.scoring.hbonds.HBondSet: #B 56 LEU N B 6 LEU O 1.66 162.8 157.9 174.1 1.000 -0.718\ncore.scoring.hbonds.HBondSet: #B 79 LEU N B 7 VAL O 1.74 157.3 152.8 147.5 1.000 -0.891\ncore.scoring.hbonds.HBondSet: #B 7 VAL N B 77 GLY O 2.02 174.4 161.6 166.4 1.000 -1.357\ncore.scoring.hbonds.HBondSet: #B 58 THR N B 8 VAL O 2.72 146.2 149.3 -11.1 1.000 -0.011\ncore.scoring.hbonds.HBondSet: #B 8 VAL N B 56 LEU O 1.97 177.7 162.1 69.5 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 9 VAL N B 79 LEU O 1.99 152.6 143.2 57.5 1.000 -1.020\ncore.scoring.hbonds.HBondSet: #B 81 VAL N B 9 VAL O 1.91 177.5 153.5 -123.6 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #B 14 VAL N B 11 ALA O 2.39 160.5 137.3 -127.2 1.000 -0.898\ncore.scoring.hbonds.HBondSet: #B 19 LEU N B 15 GLY O 1.91 147.7 148.4 -139.0 1.000 -0.998\ncore.scoring.hbonds.HBondSet: #B 20 THR N B 16 LYS O 1.82 178.0 165.1 -147.9 1.000 -1.102\ncore.scoring.hbonds.HBondSet: #B 21 ILE N B 17 SER O 1.94 143.6 134.8 -118.0 1.000 -0.775\ncore.scoring.hbonds.HBondSet: #B 17 SER OG B 57 ASP OD2 2.05 111.8 116.7 177.1 1.000 -0.366\ncore.scoring.hbonds.HBondSet: #B 22 GLN N B 18 ALA O 1.97 153.3 145.9 -100.8 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #B 23 LEU N B 19 LEU O 2.30 169.7 154.3 -159.7 1.000 -1.230\ncore.scoring.hbonds.HBondSet: #B 24 ILE N B 20 THR O 2.14 171.9 143.2 -132.6 1.000 -1.403\ncore.scoring.hbonds.HBondSet: #B 25 GLN N B 21 ILE O 1.99 147.2 133.1 -81.7 1.000 -0.687\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 21 ILE O 2.58 123.3 138.4 -158.7 1.000 -0.044\ncore.scoring.hbonds.HBondSet: #B 26 ASN N B 22 GLN O 1.79 133.6 118.3 -62.9 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #B 38 ASP N B 57 ASP O 1.85 160.4 146.8 -3.4 1.000 -1.515\ncore.scoring.hbonds.HBondSet: #B 57 ASP N B 38 ASP O 1.89 149.2 160.7 -105.2 1.000 -0.676\ncore.scoring.hbonds.HBondSet: #B 40 TYR N B 55 ILE O 2.11 143.2 150.5 52.1 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #B 55 ILE N B 40 TYR O 2.12 137.4 137.0 -91.8 1.000 -0.380\ncore.scoring.hbonds.HBondSet: #B 42 LYS N B 53 LEU O 1.91 134.3 138.2 49.9 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #B 44 VAL N B 51 CYS O 1.91 173.0 163.2 -19.0 1.000 -1.262\ncore.scoring.hbonds.HBondSet: #B 51 CYS N B 44 VAL O 1.70 159.6 163.0 112.3 1.000 -0.521\ncore.scoring.hbonds.HBondSet: #B 46 ILE N B 49 GLU O 1.89 149.1 141.5 15.9 1.000 -1.413\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 46 ILE O 1.91 143.8 123.3 -75.0 0.835 -0.513\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD2 2.06 128.7 100.1 -167.7 0.718 -0.614\ncore.scoring.hbonds.HBondSet: #B 161 ARG NH1B 47 ASP OD1 1.97 118.9 114.3 145.6 0.718 -0.498\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH1B 47 ASP OD2 1.52 144.2 128.2 -31.0 0.741 -0.595\ncore.scoring.hbonds.HBondSet: #B 164 ARG NE B 49 GLU OE1 2.22 142.9 142.9 -117.5 0.788 -0.542\ncore.scoring.hbonds.HBondSet: #B 164 ARG NH2B 49 GLU OE1 2.04 151.6 123.3 -27.3 0.788 -1.398\ncore.scoring.hbonds.HBondSet: #B 63 GLU N B 62 GLU OE2 2.31 142.0 107.1 -34.1 0.341 -0.378\ncore.scoring.hbonds.HBondSet: #B 68 ARG N B 64 TYR O 2.21 159.0 142.6 -170.1 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #B 66 ALA N B 68 ARG O 2.47 136.1 106.6 33.2 1.000 -0.418\ncore.scoring.hbonds.HBondSet: #B 69 ASP N B 67 MET O 1.74 106.9 117.0 -154.2 1.000 -0.195\ncore.scoring.hbonds.HBondSet: #B 70 GLN N B 67 MET O 1.98 119.6 120.4 -45.6 1.000 -0.524\ncore.scoring.hbonds.HBondSet: #B 71 TYR N B 67 MET O 2.16 162.9 149.0 67.5 1.000 -1.022\ncore.scoring.hbonds.HBondSet: #B 73 ARG N B 69 ASP O 2.51 126.5 117.9 -129.1 1.000 -0.007\ncore.scoring.hbonds.HBondSet: #B 73 ARG NH2B 69 ASP OD1 2.57 139.8 133.2 -39.3 0.459 -0.260\ncore.scoring.hbonds.HBondSet: #B 74 THR N B 70 GLN O 2.49 146.7 125.7 -106.1 1.000 -0.149\ncore.scoring.hbonds.HBondSet: #B 75 GLY N B 71 TYR O 1.87 145.5 145.5 -114.3 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #B 112 VAL N B 78 PHE O 2.16 146.2 176.3 179.0 1.000 -0.584\ncore.scoring.hbonds.HBondSet: #B 78 PHE N B 110 PRO O 2.04 158.2 134.9 -140.7 1.000 -1.502\ncore.scoring.hbonds.HBondSet: #B 114 VAL N B 80 CYS O 1.97 165.7 143.0 81.3 1.000 -1.057\ncore.scoring.hbonds.HBondSet: #B 80 CYS N B 112 VAL O 1.96 160.5 171.4 -82.6 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 116 ASN N B 82 PHE O 2.01 161.1 144.6 -120.6 1.000 -1.162\ncore.scoring.hbonds.HBondSet: #B 86 ASN N B 83 ALA O 1.81 161.3 117.4 -107.2 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #B 83 ALA N B 89 SER OG 1.96 171.4 124.8 149.0 1.000 -2.326\ncore.scoring.hbonds.HBondSet: #B 84 ILE N B 116 ASN O 1.99 170.8 165.9 28.4 1.000 -1.215\ncore.scoring.hbonds.HBondSet: #B 124 THR N B 84 ILE O 2.25 143.4 147.0 -164.4 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 89 SER N B 86 ASN OD1 1.35 169.0 136.5 -89.4 0.929 -0.473\ncore.scoring.hbonds.HBondSet: #B 90 PHE N B 86 ASN O 2.39 149.6 128.9 -139.9 1.000 -0.954\ncore.scoring.hbonds.HBondSet: #B 87 THR OG1B 124 THR OG1 1.94 120.7 134.4 95.7 0.576 -0.105\ncore.scoring.hbonds.HBondSet: #B 91 GLU N B 87 THR O 1.86 159.4 146.8 -126.5 1.000 -1.080\ncore.scoring.hbonds.HBondSet: #B 92 ASP N B 88 LYS O 2.02 132.2 148.3 -133.4 1.000 -0.579\ncore.scoring.hbonds.HBondSet: #B 96 TYR N B 92 ASP O 2.17 155.0 146.9 149.5 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #B 97 ARG N B 93 ILE O 2.00 161.9 151.3 -100.5 1.000 -1.005\ncore.scoring.hbonds.HBondSet: #B 98 GLU N B 94 HIS O 2.09 144.5 133.0 -121.8 1.000 -0.859\ncore.scoring.hbonds.HBondSet: #B 99 GLN N B 95 GLN O 1.75 174.2 171.9 -172.4 1.000 -0.848\ncore.scoring.hbonds.HBondSet: #B 100 ILE N B 96 TYR O 1.99 154.7 141.5 -129.9 1.000 -1.183\ncore.scoring.hbonds.HBondSet: #B 97 ARG NH1B 98 GLU OE1 2.08 102.1 136.3 167.3 0.600 -0.281\ncore.scoring.hbonds.HBondSet: #B 101 LYS N B 97 ARG O 2.20 169.3 146.3 -103.0 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #B 102 ARG N B 98 GLU O 2.10 155.0 157.1 -125.1 1.000 -0.944\ncore.scoring.hbonds.HBondSet: #B 103 VAL N B 99 GLN O 2.07 144.8 153.9 -148.4 1.000 -0.924\ncore.scoring.hbonds.HBondSet: #B 104 LYS N B 101 LYS O 2.32 156.3 98.4 -104.6 1.000 -0.333\ncore.scoring.hbonds.HBondSet: #B 105 ASP N B 101 LYS O 1.87 114.7 134.2 -113.9 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 106 SER N B 104 LYS O 2.12 146.8 90.6 135.1 1.000 -0.382\ncore.scoring.hbonds.HBondSet: #B 142 ILE N B 113 LEU O 2.29 151.5 148.5 168.3 1.000 -1.122\ncore.scoring.hbonds.HBondSet: #B 113 LEU N B 140 PRO O 2.26 166.9 142.6 -106.9 1.000 -0.939\ncore.scoring.hbonds.HBondSet: #B 115 GLY N B 142 ILE O 1.89 175.4 163.3 115.9 1.000 -1.115\ncore.scoring.hbonds.HBondSet: #B 144 THR N B 115 GLY O 1.82 166.4 143.8 108.2 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #B 116 ASN ND2B 144 THR OG1 2.11 151.9 114.3 74.4 1.000 -1.625\ncore.scoring.hbonds.HBondSet: #B 120 LEU N B 117 LYS O 1.61 160.9 146.4 -148.9 1.000 -0.638\ncore.scoring.hbonds.HBondSet: #B 118 CYS N B 144 THR O 2.26 149.6 158.9 128.3 1.000 -0.664\ncore.scoring.hbonds.HBondSet: #B 122 ALA N B 120 LEU O 2.39 118.6 115.2 -135.1 1.000 -0.091\ncore.scoring.hbonds.HBondSet: #B 123 ARG NE B 125 VAL O 1.27 158.8 151.8 151.1 0.859 -0.468\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH1B 143 GLU OE1 2.43 152.6 131.2 154.5 0.835 -1.002\ncore.scoring.hbonds.HBondSet: #B 123 ARG NH2B 143 GLU OE2 2.05 144.9 97.4 -150.9 0.835 -0.765\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 126 GLU O 2.05 144.5 148.6 -178.6 1.000 -1.206\ncore.scoring.hbonds.HBondSet: #B 126 GLU N B 129 GLN OE1 1.82 136.4 92.4 58.0 0.482 -0.121\ncore.scoring.hbonds.HBondSet: #B 129 GLN N B 126 GLU O 2.06 119.8 113.4 -80.2 1.000 -0.010\ncore.scoring.hbonds.HBondSet: #B 128 ARG NH2B 127 SER OG 1.74 118.8 110.7 98.3 0.435 -0.082\ncore.scoring.hbonds.HBondSet: #B 130 ALA N B 127 SER O 1.83 123.3 115.7 -86.8 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 131 GLN N B 127 SER O 1.62 168.0 152.9 134.3 1.000 -0.522\ncore.scoring.hbonds.HBondSet: #B 132 ASP N B 128 ARG O 1.71 157.8 144.0 -118.8 1.000 -0.662\ncore.scoring.hbonds.HBondSet: #B 133 LEU N B 129 GLN O 2.33 152.8 121.1 -102.2 1.000 -0.556\ncore.scoring.hbonds.HBondSet: #B 134 ALA N B 130 ALA O 1.84 166.9 159.5 -175.0 1.000 -1.226\ncore.scoring.hbonds.HBondSet: #B 135 ARG N B 131 GLN O 1.92 146.8 146.1 -91.4 1.000 -0.623\ncore.scoring.hbonds.HBondSet: #B 136 SER N B 132 ASP O 2.11 155.5 152.5 -172.9 1.000 -1.320\ncore.scoring.hbonds.HBondSet: #B 137 TYR N B 133 LEU O 2.17 133.9 144.9 -123.0 1.000 -0.463\ncore.scoring.hbonds.HBondSet: #B 138 GLY N B 134 ALA O 1.85 135.9 139.4 -133.7 1.000 -0.690\ncore.scoring.hbonds.HBondSet: #B 139 ILE N B 134 ALA O 1.78 172.1 146.2 58.4 1.000 -1.059\ncore.scoring.hbonds.HBondSet: #B 141 TYR OH B 143 GLU OE2 1.30 169.7 124.0 -22.7 0.953 -1.194\ncore.scoring.hbonds.HBondSet: #B 149 ARG N B 145 SER O 1.85 110.9 146.3 -130.1 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #B 148 THR N B 145 SER OG 2.10 165.0 108.1 -79.1 0.694 -2.084\ncore.scoring.hbonds.HBondSet: #B 145 SER N B 150 GLN O 1.80 163.2 158.2 -5.1 1.000 -1.148\ncore.scoring.hbonds.HBondSet: #B 150 GLN N B 148 THR OG1 2.31 163.9 114.4 48.9 0.576 -1.417\ncore.scoring.hbonds.HBondSet: #B 152 VAL N B 149 ARG O 2.57 162.8 114.6 -116.9 1.000 -0.414\ncore.scoring.hbonds.HBondSet: #B 155 ALA N B 151 GLY O 1.98 152.5 142.8 -118.1 1.000 -0.965\ncore.scoring.hbonds.HBondSet: #B 156 PHE N B 152 VAL O 2.52 168.0 149.9 -128.4 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #B 157 TYR N B 153 GLU O 2.01 159.5 148.4 -101.6 1.000 -0.968\ncore.scoring.hbonds.HBondSet: #B 158 THR N B 154 ASP O 1.96 151.7 136.5 -81.7 1.000 -0.789\ncore.scoring.hbonds.HBondSet: #B 159 LEU N B 155 ALA O 2.49 137.7 130.1 -132.6 1.000 -0.327\ncore.scoring.hbonds.HBondSet: #B 160 VAL N B 156 PHE O 2.28 136.6 138.3 -137.9 1.000 -0.671\ncore.scoring.hbonds.HBondSet: #B 161 ARG N B 157 TYR O 2.05 160.9 147.4 -145.4 1.000 -1.405\ncore.scoring.hbonds.HBondSet: #B 162 GLU N B 158 THR O 1.98 142.2 135.1 -129.6 1.000 -0.935\ncore.scoring.hbonds.HBondSet: #B 163 ILE N B 159 LEU O 2.27 145.9 130.6 -115.9 1.000 -0.628\ncore.scoring.hbonds.HBondSet: #B 164 ARG N B 160 VAL O 1.87 170.6 168.8 -122.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #B 165 GLN N B 161 ARG O 1.97 158.8 148.5 -96.5 1.000 -0.933\ncore.scoring.hbonds.HBondSet: #B 166 HIS N B 162 GLU O 2.15 141.4 126.0 -121.4 1.000 -0.756\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 163 ILE O 2.28 116.2 139.1 -144.3 1.000 -0.241\ncore.scoring.hbonds.HBondSet: #B 167 LYS N B 164 ARG O 2.22 148.2 99.2 -95.0 1.000 -0.254\ncore.scoring.hbonds.HBondSet: #B 168 LEU N B 165 GLN O 2.06 156.0 105.9 -96.2 1.000 -0.731\ncore.scoring.hbonds.HBondSet: #B 165 GLN NE2B 169 ARG O 2.02 154.2 163.2 -90.6 0.600 -0.731\ncore.scoring.hbonds.HBondSet: #C 2 THR N C 50 THR O 1.72 154.1 148.6 160.0 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 52 LEU N C 2 THR O 1.55 161.2 156.3 126.4 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #C 4 TYR OH C 49 GLU OE1 1.43 137.8 91.5 160.8 0.859 -0.322\ncore.scoring.hbonds.HBondSet: #C 4 TYR N C 52 LEU O 2.12 158.0 146.8 110.8 1.000 -0.956\ncore.scoring.hbonds.HBondSet: #C 54 ASP N C 4 TYR O 2.02 153.2 152.3 86.2 1.000 -0.814\ncore.scoring.hbonds.HBondSet: #C 5 LYS N C 76 GLU OE1 1.63 176.7 141.4 -69.2 0.718 -1.026\ncore.scoring.hbonds.HBondSet: #C 76 GLU N C 5 LYS O 1.69 153.2 142.2 -29.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #C 77 GLY N C 5 LYS O 2.17 159.7 146.5 136.1 1.000 -1.218\ncore.scoring.hbonds.HBondSet: #C 6 LEU N C 54 ASP O 2.32 137.6 138.1 85.2 1.000 -0.152\ncore.scoring.hbonds.HBondSet: #C 56 LEU N C 6 LEU O 1.75 173.5 163.1 -159.7 1.000 -0.981\ncore.scoring.hbonds.HBondSet: #C 7 VAL N C 77 GLY O 2.04 157.7 156.7 -176.3 1.000 -1.280\ncore.scoring.hbonds.HBondSet: #C 79 LEU N C 7 VAL O 2.04 161.1 151.4 106.5 1.000 -1.011\ncore.scoring.hbonds.HBondSet: #C 8 VAL N C 56 LEU O 1.70 168.1 175.5 -29.1 1.000 -0.633\ncore.scoring.hbonds.HBondSet: #C 58 THR N C 8 VAL O 2.51 149.3 152.2 -34.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #C 81 VAL N C 9 VAL O 1.97 169.4 138.7 -95.1 1.000 -1.087\ncore.scoring.hbonds.HBondSet: #C 9 VAL N C 79 LEU O 1.99 163.0 158.5 69.8 1.000 -1.041\ncore.scoring.hbonds.HBondSet: #C 14 VAL N C 11 ALA O 2.53 152.2 138.8 -142.7 1.000 -0.663\ncore.scoring.hbonds.HBondSet: #C 116 ASN ND2C 14 VAL O 1.82 167.4 146.4 -179.9 1.000 -1.537\ncore.scoring.hbonds.HBondSet: #C 20 THR N C 16 LYS O 1.99 167.4 144.5 -123.1 1.000 -1.282\ncore.scoring.hbonds.HBondSet: #C 21 ILE N C 17 SER O 1.82 165.5 158.8 -113.3 1.000 -0.929\ncore.scoring.hbonds.HBondSet: #C 22 GLN N C 18 ALA O 2.38 136.0 129.7 -113.7 1.000 -0.171\ncore.scoring.hbonds.HBondSet: #C 23 LEU N C 19 LEU O 2.36 161.8 147.0 -120.0 1.000 -0.796\ncore.scoring.hbonds.HBondSet: #C 24 ILE N C 20 THR O 2.00 166.6 151.1 -111.1 1.000 -1.125\ncore.scoring.hbonds.HBondSet: #C 25 GLN N C 21 ILE O 1.72 154.7 129.3 -67.1 1.000 -0.607\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 21 ILE O 2.57 119.1 135.6 -156.2 1.000 -0.015\ncore.scoring.hbonds.HBondSet: #C 26 ASN N C 22 GLN O 1.79 133.4 103.5 -60.3 1.000 -0.147\ncore.scoring.hbonds.HBondSet: #C 22 GLN NE2C 146 ALA O 1.63 154.0 167.5 -163.7 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #C 149 ARG NE C 22 GLN O 2.21 140.1 113.0 69.0 0.812 -0.272\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 22 GLN O 1.88 151.2 126.3 147.7 0.812 -1.210\ncore.scoring.hbonds.HBondSet: #C 42 LYS NZ C 23 LEU O 1.67 132.9 144.5 165.1 0.812 -0.372\ncore.scoring.hbonds.HBondSet: #C 27 HIS NE2C 25 GLN OE1 1.52 162.8 154.3 6.2 0.435 -1.662\ncore.scoring.hbonds.HBondSet: #C 38 ASP N C 57 ASP O 2.03 155.3 145.6 -28.1 1.000 -1.404\ncore.scoring.hbonds.HBondSet: #C 57 ASP N C 38 ASP O 1.79 175.4 159.9 -62.4 1.000 -0.987\ncore.scoring.hbonds.HBondSet: #C 41 ARG NE C 40 TYR O 1.84 155.4 116.2 116.0 0.671 -0.817\ncore.scoring.hbonds.HBondSet: #C 40 TYR N C 55 ILE O 2.07 139.9 138.2 60.9 1.000 -0.682\ncore.scoring.hbonds.HBondSet: #C 55 ILE N C 40 TYR O 2.01 140.2 128.7 -92.3 1.000 -0.492\ncore.scoring.hbonds.HBondSet: #C 42 LYS N C 53 LEU O 1.92 154.7 134.6 29.2 1.000 -1.568\ncore.scoring.hbonds.HBondSet: #C 53 LEU N C 42 LYS O 1.68 151.6 151.7 111.2 1.000 -0.308\ncore.scoring.hbonds.HBondSet: #C 44 VAL N C 51 CYS O 1.85 164.6 152.3 -11.9 1.000 -1.400\ncore.scoring.hbonds.HBondSet: #C 51 CYS N C 44 VAL O 1.80 154.4 157.7 -123.0 1.000 -0.742\ncore.scoring.hbonds.HBondSet: #C 46 ILE N C 49 GLU O 1.67 145.0 151.1 -29.9 1.000 -0.420\ncore.scoring.hbonds.HBondSet: #C 161 ARG NE C 47 ASP OD2 1.79 167.7 111.2 -154.9 0.741 -1.399\ncore.scoring.hbonds.HBondSet: #C 161 ARG NH2C 47 ASP OD1 1.31 152.2 114.3 134.3 0.741 -0.155\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH1C 47 ASP OD2 1.79 144.3 119.0 -34.0 0.694 -1.005\ncore.scoring.hbonds.HBondSet: #C 164 ARG NE C 49 GLU OE1 2.09 148.3 123.1 -106.5 0.765 -0.680\ncore.scoring.hbonds.HBondSet: #C 164 ARG NH2C 49 GLU OE1 1.98 150.7 130.9 -21.0 0.765 -1.389\ncore.scoring.hbonds.HBondSet: #C 64 TYR N C 61 GLN O 2.09 163.3 134.6 -104.2 1.000 -1.046\ncore.scoring.hbonds.HBondSet: #C 67 MET N C 64 TYR O 2.24 163.1 120.2 -110.8 1.000 -0.992\ncore.scoring.hbonds.HBondSet: #C 68 ARG N C 65 SER O 2.45 162.1 114.3 -110.9 1.000 -0.588\ncore.scoring.hbonds.HBondSet: #C 71 TYR N C 67 MET O 2.78 160.9 130.8 -139.3 1.000 -0.124\ncore.scoring.hbonds.HBondSet: #C 72 MET N C 68 ARG O 1.90 156.3 161.6 -113.6 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 68 ARG NH1C 99 GLN OE1 2.34 152.0 138.5 126.6 0.718 -0.553\ncore.scoring.hbonds.HBondSet: #C 73 ARG N C 69 ASP O 2.24 126.8 126.8 -125.2 1.000 -0.354\ncore.scoring.hbonds.HBondSet: #C 74 THR N C 70 GLN O 2.31 145.5 139.3 -134.5 1.000 -0.795\ncore.scoring.hbonds.HBondSet: #C 75 GLY N C 71 TYR O 2.01 145.7 143.8 -113.0 1.000 -0.744\ncore.scoring.hbonds.HBondSet: #C 78 PHE N C 110 PRO O 1.89 171.1 154.0 -133.0 1.000 -1.258\ncore.scoring.hbonds.HBondSet: #C 112 VAL N C 78 PHE O 2.26 137.9 153.6 -177.7 1.000 -0.706\ncore.scoring.hbonds.HBondSet: #C 114 VAL N C 80 CYS O 1.86 155.0 164.5 88.3 1.000 -0.760\ncore.scoring.hbonds.HBondSet: #C 80 CYS N C 112 VAL O 1.88 162.1 169.5 2.0 1.000 -1.001\ncore.scoring.hbonds.HBondSet: #C 82 PHE N C 114 VAL O 1.97 151.0 151.7 -114.5 1.000 -0.844\ncore.scoring.hbonds.HBondSet: #C 116 ASN N C 82 PHE O 1.73 153.8 170.9 -52.7 1.000 -0.479\ncore.scoring.hbonds.HBondSet: #C 86 ASN N C 83 ALA O 2.10 150.9 123.3 -107.8 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #C 83 ALA N C 89 SER OG 2.04 170.4 133.9 145.8 1.000 -2.012\ncore.scoring.hbonds.HBondSet: #C 84 ILE N C 116 ASN O 1.95 159.3 172.6 -73.4 1.000 -0.931\ncore.scoring.hbonds.HBondSet: #C 124 THR N C 84 ILE O 1.76 153.0 166.8 -131.8 1.000 -0.587\ncore.scoring.hbonds.HBondSet: #C 125 VAL N C 84 ILE O 2.53 164.3 138.7 -65.9 1.000 -0.489\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN O 2.24 126.7 121.2 -94.4 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #C 89 SER N C 86 ASN OD1 2.15 151.2 132.2 -37.0 0.976 -1.308\ncore.scoring.hbonds.HBondSet: #C 90 PHE N C 86 ASN O 2.49 148.3 136.9 172.5 1.000 -1.021\ncore.scoring.hbonds.HBondSet: #C 91 GLU N C 87 THR O 1.73 168.1 160.6 -136.9 1.000 -0.842\ncore.scoring.hbonds.HBondSet: #C 92 ASP N C 88 LYS O 1.77 142.1 145.1 -143.0 1.000 -0.721\ncore.scoring.hbonds.HBondSet: #C 93 ILE N C 89 SER O 2.27 134.8 151.0 -133.2 1.000 -0.401\ncore.scoring.hbonds.HBondSet: #C 95 GLN N C 92 ASP O 2.18 123.3 117.3 -80.6 1.000 -0.020\ncore.scoring.hbonds.HBondSet: #C 96 TYR N C 92 ASP O 2.15 160.9 154.3 168.7 1.000 -1.329\ncore.scoring.hbonds.HBondSet: #C 97 ARG N C 93 ILE O 1.67 175.6 168.1 -141.3 1.000 -0.605\ncore.scoring.hbonds.HBondSet: #C 98 GLU N C 94 HIS O 2.15 153.5 139.2 -126.1 1.000 -1.058\ncore.scoring.hbonds.HBondSet: #C 99 GLN N C 95 GLN O 2.33 146.1 145.4 -117.0 1.000 -0.482\ncore.scoring.hbonds.HBondSet: #C 100 ILE N C 96 TYR O 2.09 167.1 158.5 -150.8 1.000 -1.289\ncore.scoring.hbonds.HBondSet: #C 101 LYS N C 97 ARG O 2.11 163.6 148.7 -126.8 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #C 102 ARG N C 98 GLU O 2.14 156.4 133.1 -120.4 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #C 103 VAL N C 99 GLN O 1.77 170.6 155.8 -107.8 1.000 -0.867\ncore.scoring.hbonds.HBondSet: #C 104 LYS N C 100 ILE O 1.74 161.0 159.6 -109.4 1.000 -0.667\ncore.scoring.hbonds.HBondSet: #C 106 SER N C 101 LYS O 2.41 142.0 129.0 1.7 1.000 -1.169\ncore.scoring.hbonds.HBondSet: #C 102 ARG NH2C 105 ASP OD1 2.37 145.4 152.0 -158.6 0.318 -0.641\ncore.scoring.hbonds.HBondSet: #C 108 ASP N C 106 SER OG 2.22 135.0 142.4 -10.1 0.482 -0.020\ncore.scoring.hbonds.HBondSet: #C 169 ARG NH1C 108 ASP OD2 1.70 129.9 173.3 -0.5 0.412 -0.001\ncore.scoring.hbonds.HBondSet: #C 142 ILE N C 113 LEU O 1.88 166.1 166.9 171.9 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #C 113 LEU N C 140 PRO O 1.93 164.7 144.6 -108.0 1.000 -1.073\ncore.scoring.hbonds.HBondSet: #C 115 GLY N C 142 ILE O 2.04 164.1 154.8 175.7 1.000 -1.446\ncore.scoring.hbonds.HBondSet: #C 144 THR N C 115 GLY O 2.02 173.4 137.2 103.8 1.000 -1.173\ncore.scoring.hbonds.HBondSet: #C 120 LEU N C 117 LYS O 1.80 177.0 133.7 -108.6 1.000 -1.051\ncore.scoring.hbonds.HBondSet: #C 118 CYS N C 144 THR O 1.85 163.3 151.8 126.7 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH1C 143 GLU OE1 2.17 169.7 110.4 151.0 0.765 -1.461\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 143 GLU OE2 1.91 161.0 121.8 -138.6 0.765 -1.288\ncore.scoring.hbonds.HBondSet: #C 123 ARG NE C 125 VAL O 2.03 131.2 124.9 118.0 0.718 -0.374\ncore.scoring.hbonds.HBondSet: #C 123 ARG NH2C 125 VAL O 1.68 140.4 134.2 -140.9 0.718 -0.735\ncore.scoring.hbonds.HBondSet: #C 130 ALA N C 126 GLU O 2.53 165.6 156.0 -159.6 1.000 -0.707\ncore.scoring.hbonds.HBondSet: #C 131 GLN N C 127 SER O 1.87 164.3 151.0 -110.2 1.000 -1.010\ncore.scoring.hbonds.HBondSet: #C 132 ASP N C 128 ARG O 2.01 146.5 132.7 -107.0 1.000 -0.738\ncore.scoring.hbonds.HBondSet: #C 133 LEU N C 129 GLN O 1.98 143.1 129.4 -112.3 1.000 -0.717\ncore.scoring.hbonds.HBondSet: #C 134 ALA N C 130 ALA O 1.82 166.4 162.3 -156.9 1.000 -1.089\ncore.scoring.hbonds.HBondSet: #C 135 ARG N C 131 GLN O 2.10 173.9 148.9 -111.9 1.000 -1.178\ncore.scoring.hbonds.HBondSet: #C 135 ARG NH1C 132 ASP OD1 2.38 136.5 145.6 -62.9 0.647 -0.181\ncore.scoring.hbonds.HBondSet: #C 136 SER N C 132 ASP O 2.12 152.8 137.7 -125.8 1.000 -1.072\ncore.scoring.hbonds.HBondSet: #C 137 TYR N C 133 LEU O 1.85 167.1 151.6 -134.6 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #C 139 ILE N C 134 ALA O 1.96 155.3 118.9 78.3 1.000 -0.895\ncore.scoring.hbonds.HBondSet: #C 141 TYR N D 43 GLN OE1 2.04 144.7 105.1 -161.4 0.882 -1.464\ncore.scoring.hbonds.HBondSet: #D 43 GLN NE2C 141 TYR O 2.03 157.6 130.4 65.6 0.882 -0.956\ncore.scoring.hbonds.HBondSet: #C 141 TYR OH C 143 GLU OE2 1.55 152.8 103.6 -1.4 0.929 -1.224\ncore.scoring.hbonds.HBondSet: #C 148 THR N C 145 SER OG 2.52 155.7 104.8 -76.2 0.718 -0.373\ncore.scoring.hbonds.HBondSet: #C 145 SER N C 150 GLN O 2.05 141.0 168.7 41.9 1.000 -0.559\ncore.scoring.hbonds.HBondSet: #C 152 VAL N C 149 ARG O 2.51 168.9 127.3 -107.7 1.000 -0.552\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH1C 153 GLU OE2 1.56 159.7 126.3 71.8 0.600 -0.384\ncore.scoring.hbonds.HBondSet: #C 149 ARG NH2C 153 GLU OE2 2.54 125.7 139.4 -17.5 0.600 -0.123\ncore.scoring.hbonds.HBondSet: #C 155 ALA N C 151 GLY O 1.78 146.1 133.1 -129.0 1.000 -0.800\ncore.scoring.hbonds.HBondSet: #C 156 PHE N C 152 VAL O 1.89 154.0 157.7 -140.7 1.000 -0.980\ncore.scoring.hbonds.HBondSet: #C 157 TYR N C 153 GLU O 1.84 163.0 153.4 -86.5 1.000 -0.888\ncore.scoring.hbonds.HBondSet: #C 158 THR N C 154 ASP O 1.94 154.1 142.2 -89.4 1.000 -0.813\ncore.scoring.hbonds.HBondSet: #C 159 LEU N C 155 ALA O 2.54 144.2 134.9 -128.1 1.000 -0.262\ncore.scoring.hbonds.HBondSet: #C 160 VAL N C 156 PHE O 2.21 149.1 137.4 -143.0 1.000 -1.172\ncore.scoring.hbonds.HBondSet: #C 161 ARG N C 157 TYR O 1.89 162.8 155.6 -160.3 1.000 -1.302\ncore.scoring.hbonds.HBondSet: #C 162 GLU N C 158 THR O 1.95 165.7 151.2 -131.2 1.000 -1.263\ncore.scoring.hbonds.HBondSet: #C 163 ILE N C 159 LEU O 2.23 149.1 141.0 -119.3 1.000 -0.761\ncore.scoring.hbonds.HBondSet: #C 164 ARG N C 160 VAL O 1.88 171.9 160.2 -115.2 1.000 -1.091\ncore.scoring.hbonds.HBondSet: #C 165 GLN N C 161 ARG O 1.82 176.3 172.4 -139.7 1.000 -0.999\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 162 GLU OE1 1.82 144.1 91.7 156.6 0.976 -0.691\ncore.scoring.hbonds.HBondSet: #C 166 HIS N C 162 GLU O 1.92 156.4 138.7 -120.0 1.000 -1.074\ncore.scoring.hbonds.HBondSet: #C 167 LYS N C 163 ILE O 2.12 124.3 130.8 -138.7 1.000 -0.641\ncore.scoring.hbonds.HBondSet: #C 168 LEU N C 164 ARG O 1.86 161.1 155.6 -106.6 1.000 -0.912\ncore.scoring.hbonds.HBondSet: #C 169 ARG N C 165 GLN O 2.29 139.6 150.6 -146.4 1.000 -0.622\ncore.scoring.hbonds.HBondSet: #D 1 MET N C 165 GLN OE1 2.12 146.2 99.8 128.5 0.835 -0.554\ncore.scoring.hbonds.HBondSet: #C 171 LEU N C 168 LEU O 1.81 154.8 164.8 -70.6 1.000 -0.694\ncore.scoring.hbonds.HBondSet: #C 170 LYS NZ C 169 ARG O 1.86 133.9 108.9 117.0 0.224 -0.059\ncore.scoring.hbonds.HBondSet: #D 2 THR N D 50 THR O 1.98 153.0 167.9 155.1 1.000 -0.894\ncore.scoring.hbonds.HBondSet: #D 52 LEU N D 2 THR O 1.72 167.6 145.5 124.6 1.000 -0.897\ncore.scoring.hbonds.HBondSet: #D 4 TYR OH D 49 GLU OE1 1.87 148.2 90.6 -158.3 0.882 -0.520\ncore.scoring.hbonds.HBondSet: #D 4 TYR N D 52 LEU O 1.66 165.8 167.6 97.1 1.000 -0.435\ncore.scoring.hbonds.HBondSet: #D 54 ASP N D 4 TYR O 1.72 166.4 154.7 93.8 1.000 -0.648\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 4 TYR OH 2.59 162.8 134.0 74.5 0.882 -0.402\ncore.scoring.hbonds.HBondSet: #D 77 GLY N D 5 LYS O 2.52 134.7 154.4 -178.2 1.000 -0.113\ncore.scoring.hbonds.HBondSet: #D 5 LYS N D 76 GLU OE1 1.54 165.0 142.6 22.7 0.765 -1.391\ncore.scoring.hbonds.HBondSet: #D 76 GLU N D 5 LYS O 1.91 160.2 145.4 -56.2 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 56 LEU N D 6 LEU O 1.72 178.1 168.9 -117.8 1.000 -0.751\ncore.scoring.hbonds.HBondSet: #D 6 LEU N D 54 ASP O 1.90 160.8 152.3 94.5 1.000 -0.918\ncore.scoring.hbonds.HBondSet: #D 7 VAL N D 77 GLY O 2.11 157.8 159.9 -165.5 1.000 -1.145\ncore.scoring.hbonds.HBondSet: #D 79 LEU N D 7 VAL O 1.88 166.4 146.8 124.1 1.000 -1.199\ncore.scoring.hbonds.HBondSet: #D 8 VAL N D 56 LEU O 1.77 169.6 175.1 81.8 1.000 -0.833\ncore.scoring.hbonds.HBondSet: #D 58 THR N D 8 VAL O 2.43 152.2 149.9 16.5 1.000 -0.837\ncore.scoring.hbonds.HBondSet: #D 81 VAL N D 9 VAL O 1.75 169.0 165.2 144.8 1.000 -0.869\ncore.scoring.hbonds.HBondSet: #D 9 VAL N D 79 LEU O 1.93 170.0 167.2 70.2 1.000 -1.083\ncore.scoring.hbonds.HBondSet: #D 14 VAL N D 11 ALA O 2.38 148.7 141.4 -128.6 1.000 -0.645\ncore.scoring.hbonds.HBondSet: #D 116 ASN ND2D 14 VAL O 1.67 147.0 135.1 141.6 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 19 LEU N D 15 GLY O 2.05 151.7 143.9 -99.6 1.000 -0.793\ncore.scoring.hbonds.HBondSet: #D 20 THR N D 16 LYS O 2.13 166.6 143.6 -107.4 1.000 -1.071\ncore.scoring.hbonds.HBondSet: #D 17 SER OG D 57 ASP OD2 1.87 114.6 107.7 -177.0 1.000 -0.488\ncore.scoring.hbonds.HBondSet: #D 21 ILE N D 17 SER O 1.79 154.9 149.8 -137.3 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 22 GLN N D 18 ALA O 1.86 153.5 140.6 -123.6 1.000 -0.977\ncore.scoring.hbonds.HBondSet: #D 23 LEU N D 19 LEU O 2.14 158.4 150.3 -145.1 1.000 -1.247\ncore.scoring.hbonds.HBondSet: #D 24 ILE N D 20 THR O 2.07 155.1 140.7 -108.5 1.000 -0.925\ncore.scoring.hbonds.HBondSet: #D 25 GLN N D 21 ILE O 1.56 132.7 142.6 -9.3 1.000 -0.001\ncore.scoring.hbonds.HBondSet: #D 26 ASN N D 21 ILE O 2.41 136.2 146.1 167.6 1.000 -0.601\ncore.scoring.hbonds.HBondSet: #D 149 ARG NE D 22 GLN O 2.12 139.8 117.6 63.3 0.835 -0.464\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 22 GLN O 2.01 139.9 146.0 137.3 0.835 -0.652\ncore.scoring.hbonds.HBondSet: #D 29 VAL N D 27 HIS O 2.47 111.1 116.9 -152.8 1.000 -0.086\ncore.scoring.hbonds.HBondSet: #D 59 ALA N D 37 GLU OE1 2.23 169.0 99.2 -26.6 0.647 -0.979\ncore.scoring.hbonds.HBondSet: #D 57 ASP N D 38 ASP O 2.02 159.9 148.4 112.1 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 40 TYR N D 55 ILE O 1.66 150.7 149.5 -0.6 1.000 -0.730\ncore.scoring.hbonds.HBondSet: #D 55 ILE N D 40 TYR O 1.94 155.8 135.9 -80.6 1.000 -0.876\ncore.scoring.hbonds.HBondSet: #D 41 ARG NH2D 54 ASP OD1 2.11 156.8 122.7 133.7 0.647 -1.186\ncore.scoring.hbonds.HBondSet: #D 42 LYS N D 53 LEU O 2.24 133.2 129.7 31.0 1.000 -0.930\ncore.scoring.hbonds.HBondSet: #D 53 LEU N D 42 LYS O 1.82 169.1 144.4 75.9 1.000 -0.975\ncore.scoring.hbonds.HBondSet: #D 42 LYS NZ D 157 TYR OH 2.05 139.6 157.2 168.5 0.812 -0.099\ncore.scoring.hbonds.HBondSet: #D 44 VAL N D 51 CYS O 1.90 142.6 139.5 2.6 1.000 -1.373\ncore.scoring.hbonds.HBondSet: #D 51 CYS N D 44 VAL O 1.71 161.1 161.3 18.3 1.000 -0.780\ncore.scoring.hbonds.HBondSet: #D 46 ILE N D 49 GLU O 1.90 136.6 145.3 -57.8 1.000 -0.553\ncore.scoring.hbonds.HBondSet: #D 49 GLU N D 46 ILE O 2.00 157.3 116.2 99.9 1.000 -0.922\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 46 ILE O 2.07 136.9 109.4 -56.9 0.765 -0.451\ncore.scoring.hbonds.HBondSet: #D 161 ARG NE D 47 ASP OD2 1.82 167.5 111.8 -159.4 0.718 -1.487\ncore.scoring.hbonds.HBondSet: #D 161 ARG NH2D 47 ASP OD1 1.72 157.2 113.8 147.4 0.718 -1.127\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH1D 47 ASP OD2 2.23 122.1 98.1 -39.4 0.647 -0.042\ncore.scoring.hbonds.HBondSet: #D 164 ARG NE D 49 GLU OE1 2.08 121.5 136.8 -92.4 0.765 -0.014\ncore.scoring.hbonds.HBondSet: #D 164 ARG NH2D 49 GLU OE1 1.40 140.1 138.2 49.8 0.765 -0.005\ncore.scoring.hbonds.HBondSet: #D 70 GLN N D 67 MET O 2.17 136.5 115.0 -98.6 1.000 -0.317\ncore.scoring.hbonds.HBondSet: #D 72 MET N D 68 ARG O 1.99 166.7 160.7 -170.5 1.000 -1.316\ncore.scoring.hbonds.HBondSet: #D 102 ARG NH1D 69 ASP OD2 2.19 136.9 124.8 139.4 0.459 -0.823\ncore.scoring.hbonds.HBondSet: #D 73 ARG N D 69 ASP O 1.97 140.8 139.1 -103.9 1.000 -0.550\ncore.scoring.hbonds.HBondSet: #D 74 THR N D 70 GLN O 2.16 137.2 131.6 -177.7 1.000 -1.376\ncore.scoring.hbonds.HBondSet: #D 75 GLY N D 72 MET O 2.38 158.1 105.7 -99.7 1.000 -0.419\ncore.scoring.hbonds.HBondSet: #D 78 PHE N D 110 PRO O 2.05 157.7 144.7 -143.1 1.000 -1.368\ncore.scoring.hbonds.HBondSet: #D 112 VAL N D 78 PHE O 2.10 143.2 152.5 -172.7 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 114 VAL N D 80 CYS O 1.72 164.9 149.5 117.5 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 80 CYS N D 112 VAL O 1.95 161.0 172.9 34.9 1.000 -0.982\ncore.scoring.hbonds.HBondSet: #D 82 PHE N D 114 VAL O 2.03 167.4 170.3 75.0 1.000 -1.069\ncore.scoring.hbonds.HBondSet: #D 116 ASN N D 82 PHE O 2.12 146.4 173.7 -3.8 1.000 -0.636\ncore.scoring.hbonds.HBondSet: #D 86 ASN N D 83 ALA O 2.54 144.5 114.1 -111.9 1.000 -0.035\ncore.scoring.hbonds.HBondSet: #D 83 ALA N D 89 SER OG 2.11 146.5 117.3 152.5 0.976 -1.646\ncore.scoring.hbonds.HBondSet: #D 124 THR N D 84 ILE O 1.93 160.3 139.9 136.2 1.000 -1.379\ncore.scoring.hbonds.HBondSet: #D 125 VAL N D 84 ILE O 2.05 139.0 162.4 -12.1 1.000 -0.670\ncore.scoring.hbonds.HBondSet: #D 84 ILE N D 116 ASN O 1.94 147.6 177.3 -97.9 1.000 -0.661\ncore.scoring.hbonds.HBondSet: #D 89 SER N D 86 ASN OD1 2.00 161.6 108.1 -98.8 0.906 -0.997\ncore.scoring.hbonds.HBondSet: #D 90 PHE N D 86 ASN O 2.32 158.0 145.2 -158.1 1.000 -1.243\ncore.scoring.hbonds.HBondSet: #D 91 GLU N D 87 THR O 1.78 158.6 144.7 -139.2 1.000 -1.110\ncore.scoring.hbonds.HBondSet: #D 88 LYS NZ D 91 GLU OE1 2.12 150.6 156.0 -89.7 0.459 -0.167\ncore.scoring.hbonds.HBondSet: #D 92 ASP N D 88 LYS O 1.73 149.1 145.6 -122.1 1.000 -0.547\ncore.scoring.hbonds.HBondSet: #D 93 ILE N D 90 PHE O 2.03 147.4 105.4 -96.7 1.000 -0.527\ncore.scoring.hbonds.HBondSet: #D 94 HIS N D 91 GLU O 2.28 154.2 119.5 -110.3 1.000 -0.747\ncore.scoring.hbonds.HBondSet: #D 95 GLN N D 92 ASP O 1.97 143.9 112.2 -97.6 1.000 -0.551\ncore.scoring.hbonds.HBondSet: #D 96 TYR N D 92 ASP O 2.30 161.1 156.2 175.1 1.000 -1.118\ncore.scoring.hbonds.HBondSet: #D 97 ARG N D 93 ILE O 2.05 176.1 164.5 -98.8 1.000 -1.133\ncore.scoring.hbonds.HBondSet: #D 98 GLU N D 94 HIS O 2.48 142.6 122.3 -120.3 1.000 -0.261\ncore.scoring.hbonds.HBondSet: #D 99 GLN N D 95 GLN O 1.99 161.3 153.0 -125.4 1.000 -1.136\ncore.scoring.hbonds.HBondSet: #D 100 ILE N D 96 TYR O 1.87 177.4 169.1 -152.0 1.000 -1.131\ncore.scoring.hbonds.HBondSet: #D 101 LYS N D 97 ARG O 1.86 167.3 142.3 -115.0 1.000 -1.108\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 98 GLU O 2.22 125.0 130.7 -126.1 1.000 -0.337\ncore.scoring.hbonds.HBondSet: #D 102 ARG N D 99 GLN O 2.09 133.2 99.1 -93.1 1.000 -0.018\ncore.scoring.hbonds.HBondSet: #D 103 VAL N D 99 GLN O 1.88 169.2 172.6 -128.9 1.000 -1.037\ncore.scoring.hbonds.HBondSet: #D 104 LYS N D 100 ILE O 1.81 170.9 160.9 -48.5 1.000 -1.038\ncore.scoring.hbonds.HBondSet: #D 106 SER N D 101 LYS O 2.55 140.0 125.9 -41.0 1.000 -0.377\ncore.scoring.hbonds.HBondSet: #D 108 ASP N D 106 SER OG 2.21 137.3 143.4 13.5 0.459 -0.092\ncore.scoring.hbonds.HBondSet: #D 142 ILE N D 113 LEU O 2.18 165.5 165.0 143.8 1.000 -1.054\ncore.scoring.hbonds.HBondSet: #D 113 LEU N D 140 PRO O 1.99 168.8 165.8 -121.5 1.000 -1.121\ncore.scoring.hbonds.HBondSet: #D 144 THR N D 115 GLY O 2.05 151.3 119.0 102.4 1.000 -0.815\ncore.scoring.hbonds.HBondSet: #D 115 GLY N D 142 ILE O 2.14 152.6 145.4 126.2 1.000 -0.985\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 116 ASN OD1 1.95 135.6 102.0 -56.4 1.000 -0.502\ncore.scoring.hbonds.HBondSet: #D 146 ALA N D 116 ASN OD1 2.50 148.1 139.3 174.2 1.000 -0.040\ncore.scoring.hbonds.HBondSet: #D 120 LEU N D 117 LYS O 1.73 153.1 140.1 -82.7 1.000 -0.460\ncore.scoring.hbonds.HBondSet: #D 117 LYS N D 144 THR O 2.23 116.8 127.4 -123.2 1.000 -0.076\ncore.scoring.hbonds.HBondSet: #D 118 CYS N D 144 THR O 1.88 157.5 150.5 118.9 1.000 -0.964\ncore.scoring.hbonds.HBondSet: #D 123 ARG NE D 125 VAL O 1.82 128.0 130.3 143.5 0.624 -0.648\ncore.scoring.hbonds.HBondSet: #D 130 ALA N D 126 GLU O 2.57 166.7 149.2 -153.7 1.000 -0.741\ncore.scoring.hbonds.HBondSet: #D 128 ARG NH2D 127 SER OG 2.10 123.3 96.6 53.1 0.412 -0.055\ncore.scoring.hbonds.HBondSet: #D 131 GLN N D 127 SER O 1.81 150.8 149.5 -138.0 1.000 -0.911\ncore.scoring.hbonds.HBondSet: #D 132 ASP N D 128 ARG O 1.96 143.7 138.7 -118.4 1.000 -0.770\ncore.scoring.hbonds.HBondSet: #D 133 LEU N D 129 GLN O 2.05 154.0 149.6 -123.9 1.000 -1.006\ncore.scoring.hbonds.HBondSet: #D 134 ALA N D 130 ALA O 2.04 172.6 153.4 -117.2 1.000 -1.210\ncore.scoring.hbonds.HBondSet: #D 135 ARG N D 131 GLN O 2.00 157.8 139.8 -105.8 1.000 -0.974\ncore.scoring.hbonds.HBondSet: #D 136 SER N D 132 ASP O 1.90 143.1 135.1 -132.5 1.000 -0.952\ncore.scoring.hbonds.HBondSet: #D 137 TYR N D 133 LEU O 1.93 138.5 144.3 -145.7 1.000 -0.923\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 134 ALA O 2.06 114.7 140.4 -145.1 1.000 -0.403\ncore.scoring.hbonds.HBondSet: #D 139 ILE N D 134 ALA O 1.90 169.0 134.7 69.1 1.000 -1.158\ncore.scoring.hbonds.HBondSet: #D 138 GLY N D 135 ARG O 2.19 144.5 99.6 -80.6 1.000 -0.216\ncore.scoring.hbonds.HBondSet: #D 141 TYR OH D 143 GLU OE2 1.45 141.9 141.2 32.0 0.906 -0.834\ncore.scoring.hbonds.HBondSet: #D 148 THR N D 145 SER OG 2.21 162.4 109.0 -94.6 0.718 -1.869\ncore.scoring.hbonds.HBondSet: #D 145 SER N D 150 GLN O 2.05 157.8 160.0 -28.2 1.000 -1.124\ncore.scoring.hbonds.HBondSet: #D 149 ARG N D 145 SER O 2.27 108.0 131.2 -130.5 1.000 0.000\ncore.scoring.hbonds.HBondSet: #D 150 GLN N D 148 THR OG1 2.01 159.2 116.7 54.1 0.553 -1.978\ncore.scoring.hbonds.HBondSet: #D 152 VAL N D 149 ARG O 2.08 167.7 133.5 -113.0 1.000 -1.205\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH1D 153 GLU OE2 1.72 139.9 116.1 110.6 0.624 -0.269\ncore.scoring.hbonds.HBondSet: #D 149 ARG NH2D 153 GLU OE2 2.14 128.3 171.8 -38.7 0.624 -0.141\ncore.scoring.hbonds.HBondSet: #D 155 ALA N D 151 GLY O 2.21 144.4 149.7 -122.7 1.000 -0.640\ncore.scoring.hbonds.HBondSet: #D 156 PHE N D 152 VAL O 2.49 164.9 140.1 -133.1 1.000 -0.831\ncore.scoring.hbonds.HBondSet: #D 157 TYR N D 153 GLU O 1.61 176.4 168.7 -139.5 1.000 -0.343\ncore.scoring.hbonds.HBondSet: #D 159 LEU N D 155 ALA O 2.52 140.7 130.8 -124.7 1.000 -0.182\ncore.scoring.hbonds.HBondSet: #D 160 VAL N D 156 PHE O 2.09 159.7 161.6 -154.7 1.000 -1.128\ncore.scoring.hbonds.HBondSet: #D 161 ARG N D 157 TYR O 2.63 167.6 136.4 -88.2 1.000 -0.115\ncore.scoring.hbonds.HBondSet: #D 162 GLU N D 158 THR O 2.14 149.2 143.1 -142.7 1.000 -1.147\ncore.scoring.hbonds.HBondSet: #D 163 ILE N D 159 LEU O 1.94 160.5 153.2 -126.9 1.000 -1.117\ncore.scoring.hbonds.HBondSet: #D 164 ARG N D 160 VAL O 1.61 159.8 154.1 -143.4 1.000 -0.367\ncore.scoring.hbonds.HBondSet: #D 165 GLN N D 161 ARG O 1.72 164.1 141.9 -98.0 1.000 -0.642\ncore.scoring.hbonds.HBondSet: #D 166 HIS N D 162 GLU O 1.79 161.8 144.1 -107.5 1.000 -0.839\ncore.scoring.hbonds.HBondSet: #D 167 LYS N D 163 ILE O 1.99 160.5 154.2 -112.8 1.000 -1.029\ncore.scoring.hbonds.HBondSet: #D 168 LEU N D 165 GLN O 2.12 141.5 110.2 -100.9 1.000 -0.446\ncore.scoring.hbonds.HBondSet: #D 169 ARG N D 166 HIS O 1.83 168.3 146.2 -120.5 1.000 -1.104\ncore.scoring.hbonds.HBondSet: #D 170 LYS N D 167 LYS O 2.34 150.5 125.7 -124.0 1.000 -0.782\n#Dch Dn Dres Da Ach An Ares Aa length AHDang BAHang BAtor weight energy\n#A 24 ILE N A 20 THR O 2.08 160.5 165.8 117.0 1.000 -0.979\ncore.import_pose.import_pose: File '../test/data/workshops/1YY9.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 1\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 2\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 3\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 138\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 179\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 192\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 193\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 220\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 257\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 299\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 502\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 518\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 520\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 522\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 613\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 631\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 739\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 801\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG:CtermProteinFull 824\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 959\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 1039\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 1040\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 1044\ncore.conformation.Conformation: Found disulfide between residues 6 33\ncore.conformation.Conformation: 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 namePyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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\n3775.5117010964605\nNone\n926\n407\n-1.2098840439684349\n0.10835353848860374\n1.5729435146961963\n CG \ncore.pack.pack_missing_sidechains: packing residue number 522 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 631 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 739 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 801 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 824 because of missing atom number 7 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 959 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 1039 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 1040 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 1044 because of missing atom number 7 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.pack_rotamers: built 313 rotamers at 23 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n\nFinished Workshop3test in 0:03:30.121561", "state": "passed"}, "Workshop4test": {"log": "PyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nIteration: 0 Score: 2.0620873922733125 Low Score: 1.9387244928751919\nIteration: 1 Score: 10.090309345296943 Low Score: 1.9387244928751919\nIteration: 2 Score: 9.213351860692303 Low Score: 1.9387244928751919\nIteration: 3 Score: 1.539413896292002 Low Score: 1.9387244928751919\nIteration: 4 Score: 1.539413896292002 Low Score: 1.539413896292002\nIteration: 5 Score: 1.193942866448305 Low Score: 1.539413896292002\nIteration: 6 Score: 1.366727897264676 Low Score: 1.193942866448305\nIteration: 7 Score: 1.1876372894093405 Low Score: 1.193942866448305\nIteration: 8 Score: 1.186326959581379 Low Score: 1.1876372894093405\nIteration: 9 Score: 7.500614920730135 Low Score: 1.186326959581379\nIteration: 10 Score: 1.2069275483572968 Low Score: 1.186326959581379\nIteration: 11 Score: 1.0765258275619072 Low Score: 1.186326959581379\nIteration: 12 Score: 1.2969486211885597 Low Score: 1.0765258275619072\nIteration: 13 Score: 1.4194743589616596 Low Score: 1.0765258275619072\nIteration: 14 Score: 1.4587085671187907 Low Score: 1.0765258275619072\nIteration: 15 Score: 1.4587085671187907 Low Score: 1.0765258275619072\nIteration: 16 Score: 9.701722356875075 Low Score: 1.0765258275619072\nIteration: 17 Score: 1.20620528087864 Low Score: 1.0765258275619072\nIteration: 18 Score: 1.20620528087864 Low Score: 1.0765258275619072\nIteration: 19 Score: 1.1766320906359669 Low Score: 1.0765258275619072\nIteration: 20 Score: 1.1766320906359669 Low Score: 1.0765258275619072\nIteration: 21 Score: 1.1605557459141185 Low Score: 1.0765258275619072\nIteration: 22 Score: 0.8891628991599712 Low Score: 1.0765258275619072\nIteration: 23 Score: 1.0458914577549283 Low Score: 0.8891628991599712\nIteration: 24 Score: 1.0458914577549283 Low Score: 0.8891628991599712\nIteration: 25 Score: 1.0992524533621681 Low Score: 0.8891628991599712\nIteration: 26 Score: 0.3914467848333949 Low Score: 0.8891628991599712\nIteration: 27 Score: 8.080692468807655 Low Score: 0.3914467848333949\nIteration: 28 Score: 0.3791568850599214 Low Score: 0.3914467848333949\nIteration: 29 Score: 6.047298190985206 Low Score: 0.3791568850599214\nIteration: 30 Score: 0.24837425776351996 Low Score: 0.3791568850599214\nIteration: 31 Score: 0.2843921353313519 Low Score: 0.24837425776351996\nIteration: 32 Score: 0.3089852621841658 Low Score: 0.24837425776351996\nIteration: 33 Score: 0.28780906668077044 Low Score: 0.24837425776351996\nIteration: 34 Score: 0.37214044572884397 Low Score: 0.24837425776351996\nIteration: 35 Score: 0.37214044572884397 Low Score: 0.24837425776351996\nIteration: 36 Score: 0.4350610179563734 Low Score: 0.24837425776351996\nIteration: 37 Score: 3.0609275770511992 Low Score: 0.24837425776351996\nIteration: 38 Score: 0.34692080604234654 Low Score: 0.24837425776351996\nIteration: 39 Score: 0.34692080604234654 Low Score: 0.24837425776351996\nIteration: 40 Score: 0.2319218897001445 Low Score: 0.24837425776351996\nIteration: 41 Score: 0.09251746523430349 Low Score: 0.2319218897001445\nIteration: 42 Score: 0.02703306143475448 Low Score: 0.09251746523430349\nIteration: 43 Score: 0.03421678133149708 Low Score: 0.02703306143475448\nIteration: 44 Score: -0.05096197851153672 Low Score: 0.02703306143475448\nIteration: 45 Score: -0.08008040097158187 Low Score: -0.05096197851153672\nIteration: 46 Score: -0.7641968917423583 Low Score: -0.08008040097158187\nIteration: 47 Score: -0.7680928948428063 Low Score: -0.7641968917423583\nIteration: 48 Score: -0.7746606594139287 Low Score: -0.7680928948428063\nIteration: 49 Score: -0.4943313348197691 Low Score: -0.7746606594139287\nIteration: 50 Score: -0.49027186006230306 Low Score: -0.7746606594139287\nIteration: 51 Score: -0.4457963907242357 Low Score: -0.7746606594139287\nIteration: 52 Score: -0.5809462285790472 Low Score: -0.7746606594139287\nIteration: 53 Score: -0.7069620906735485 Low Score: -0.7746606594139287\nIteration: 54 Score: -0.7252494149273003 Low Score: -0.7746606594139287\nIteration: 55 Score: -1.2998480015698703 Low Score: -0.7746606594139287\nIteration: 56 Score: 6.926073085325594 Low Score: -1.2998480015698703\nIteration: 57 Score: -1.49392098092423 Low Score: -1.2998480015698703\nIteration: 58 Score: -1.4336192663501857 Low Score: -1.49392098092423\nIteration: 59 Score: -1.2882467506554764 Low Score: -1.49392098092423\nIteration: 60 Score: -1.1183042871063114 Low Score: -1.49392098092423\nIteration: 61 Score: -1.7729879399899122 Low Score: -1.49392098092423\nIteration: 62 Score: -1.7729879399899122 Low Score: -1.7729879399899122\nIteration: 63 Score: -1.7753520889575936 Low Score: -1.7729879399899122\nIteration: 64 Score: -1.748992681864756 Low Score: -1.7753520889575936\nIteration: 65 Score: -1.4291976338424681 Low Score: -1.7753520889575936\nIteration: 66 Score: -1.4291976338424681 Low Score: -1.7753520889575936\nIteration: 67 Score: -1.4160431942496179 Low Score: -1.7753520889575936\nIteration: 68 Score: -0.32938541490019535 Low Score: -1.7753520889575936\nIteration: 69 Score: -1.3010199157033622 Low Score: -1.7753520889575936\nIteration: 70 Score: -1.4022144254824935 Low Score: -1.7753520889575936\nIteration: 71 Score: -1.3987132484447171 Low Score: -1.7753520889575936\nIteration: 72 Score: -1.8238104897938756 Low Score: -1.7753520889575936\nIteration: 73 Score: -1.836959230872587 Low Score: -1.8238104897938756\nIteration: 74 Score: -1.911580465908599 Low Score: -1.836959230872587\nIteration: 75 Score: -1.8775288090054678 Low Score: -1.911580465908599\nIteration: 76 Score: -1.978462343312129 Low Score: -1.911580465908599\nIteration: 77 Score: -1.9721553860735273 Low Score: -1.978462343312129\nIteration: 78 Score: -1.9672799688319662 Low Score: -1.978462343312129\nIteration: 79 Score: -1.8981295928907924 Low Score: -1.978462343312129\nIteration: 80 Score: -1.8035678284145904 Low Score: -1.978462343312129\nIteration: 81 Score: -1.7589154777860405 Low Score: -1.978462343312129\nIteration: 82 Score: -1.7441639686814985 Low Score: -1.978462343312129\nIteration: 83 Score: -1.7480565983521141 Low Score: -1.978462343312129\nIteration: 84 Score: -1.5790888240464018 Low Score: -1.978462343312129\nIteration: 85 Score: -1.5304872257076712 Low Score: -1.978462343312129\nIteration: 86 Score: -1.686467248369596 Low Score: -1.978462343312129\nIteration: 87 Score: -1.7004766868079244 Low Score: -1.978462343312129\nIteration: 88 Score: 3.188172450242929 Low Score: -1.978462343312129\nIteration: 89 Score: -2.476231148853098 Low Score: -1.978462343312129\nIteration: 90 Score: -2.9990148981429052 Low Score: -2.476231148853098\nIteration: 91 Score: -2.9078755984370064 Low Score: -2.9990148981429052\nIteration: 92 Score: -3.1056605291231527 Low Score: -2.9990148981429052\nIteration: 93 Score: -3.1056605291231527 Low Score: -3.1056605291231527\nIteration: 94 Score: -3.0908696716718644 Low Score: -3.1056605291231527\nIteration: 95 Score: -3.057680385197988 Low Score: -3.1056605291231527\nIteration: 96 Score: -3.128122188182595 Low Score: -3.1056605291231527\nIteration: 97 Score: -2.3568775839300846 Low Score: -3.128122188182595\nIteration: 98 Score: -3.049804911457407 Low Score: -3.128122188182595\nIteration: 99 Score: -3.062349888007956 Low Score: -3.128122188182595\n3775.5117010964605\ncore.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.40936 seconds.\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\ncore.import_pose.import_pose: File '../test/data/workshops/6Q21.clean.pdb' automatically determined to be of type PDB\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.668677 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 0.195913 seconds.\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.databaseResidue 5: LYS (LYS, K):\nBase: LYS\n Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE METALBINDING SIDECHAIN_AMINE ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H HA \n Side-chain atoms: CB CG CD CE NZ 1HB 2HB 1HG 2HG 1HD 2HD 1HE 2HE 1HZ 2HZ 3HZ \nAtom Coordinates:\n N : 20.315, 43.835, 78.015\n CA : 20.418, 42.863, 79.118\n C : 19.697, 43.46, 80.329\n O : 20.096, 44.486, 80.897\n CB : 21.858, 42.487, 79.491\n CG : 22.791, 42.176, 78.316\n CD : 22.406, 40.943, 77.485\n CE : 23.009, 40.932, 76.075\n NZ : 22.748, 42.169, 75.307\n H : 21.0493, 44.5172, 77.8902\n HA : 19.9193, 41.9417, 78.815\n 1HB : 22.3125, 43.3019, 80.0551\n 2HB : 21.8492, 41.6078, 80.1356\n 1HG : 22.8124, 43.0262, 77.6332\n 2HG : 23.8008, 42.0064, 78.6884\n 1HD : 22.7418, 40.0399, 77.9965\n 2HD : 21.3219, 40.8985, 77.3807\n 1HE : 24.088, 40.801, 76.1421\n 2HE : 22.5982, 40.0953, 75.5101\n 1HZ : 23.1708, 42.0938, 74.3926\n 2HZ : 21.751, 42.2999, 75.2069\n 3HZ : 23.1434, 42.9592, 75.7961\nMirrored relative to coordinates in ResidueType: FALSE\n\nResidue 5: LYS (LYS, K):\nBase: LYS\n Properties: POLYMER PROTEIN CANONICAL_AA POLAR CHARGED POSITIVE_CHARGE SIDECHAIN_AMINE ALPHA_AA L_AA\n Variant types:\n Main-chain atoms: N CA C \n Backbone atoms: N CA C O H \n Side-chain atoms: CB CEN\nAtom Coordinates:\n N : 20.315, 43.835, 78.015\n CA : 20.418, 42.863, 79.118\n C : 19.697, 43.46, 80.329\n O : 20.096, 44.486, 80.897\n CB : 21.8754, 42.543, 79.454\n CEN: 23.4957, 41.1851, 79.3707\n H : 21.0493, 44.5172, 77.8902\nMirrored relative to coordinates in ResidueType: FALSE\n\n-104.17784121598449\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\n: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth\nbasic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth\ncore.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/workshops/aat000_03_05.200_v1_3\n\nFinished Workshop4test in 0:05:21.853807", "state": "passed"}, "Workshop5test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.39336 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: 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/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/pyPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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.\nMover name: PyMOLMover, Mover type: MoverBase, Mover current tag:NoTag\nKeep history: True\nUpdate energy: False\nLast packet sent time: 1.6686e+09\nUpdate interval: 0\nLink: max packet size: 7678\nsent count: 2\nsocket handle: 3\nuuid shorts: 0 0 0 0 0 0 0 0 \nsocket address family: 2\nsocket address address: 16777343 : 127.0.0.1\nsocket address port: 59645 : 65000\nsocket max_packet_size: 7678\n\n\nMover name: Small, Mover type: Small, Mover current tag:NoTag\nMax angle for helices (H): 5\nMax angle for strands (E): 5\nMax angle for loops (L): 5\nTemperature factor (kT): 1\nNumber of moves: 1\n\nMover name: Shear, Mover type: Shear, Mover current tag:NoTag\nMax angle for helices (H): 0\nMax angle for strands (E): 5\nMax angle for loops (L): 6\nTemperature factor (kT): 1\nNumber of moves: 1\n\n\n-------------------------------\n resnum Type TRUE/FALSE \n-------------------------------\n DEFAULT BB FALSE\n DEFAULT SC FALSE\n DEFAULT NU FALSE\n DEFAULT BRANCH FALSE\n 050 BB TRUE\n 051 BB TRUE\n-------------------------------\n jumpnum Type TRUE/FALSE \n-------------------------------\n DEFAULT JUMP FALSE\n-------------------------------\n resnum atomnum Type TRUE/FALSE \n-------------------------------\n DEFAULT PHI FALSE\n DEFAULT THETA FALSE\n DEFAULT D FALSE\n DEFAULT RB1 FALSE\n DEFAULT RB2 FALSE\n DEFAULT RB3 FALSE\n DEFAULT RB4 FALSE\n DEFAULT RB5 FALSE\n DEFAULT RB6 FALSE\n-------------------------------\n\n\nMover name: MinMover, Mover type: MinMover, Mover current tag:NoTag\nMinimization type:\tlbfgs_armijo_nonmonotone\nScorefunction:\t\tref2015\nScore tolerance:\t0.01\nNb list:\t\tTrue\nDeriv check:\t\tFalse\nMovemap:\n\n-------------------------------\n resnum Type TRUE/FALSE \n-------------------------------\n DEFAULT BB FALSE\n DEFAULT SC FALSE\n DEFAULT NU FALSE\n DEFAULT BRANCH FALSE\n 040 BB TRUE\n 041 BB TRUE\n 042 BB TRUE\n 043 BB TRUE\n 044 BB TRUE\n 045 BB TRUE\n 046 BB TRUE\n 047 BB TRUE\n 048 BB TRUE\n 049 BB TRUE\n 050 BB TRUE\n 051 BB TRUE\n 052 BB TRUE\n 053 BB TRUE\n 054 BB TRUE\n 055 BB TRUE\n 056 BB TRUE\n 057 BB TRUE\n 058 BB TRUE\n 059 BB TRUE\n 060 BB TRUE\n-------------------------------\n jumpnum Type TRUE/FALSE \n-------------------------------\n DEFAULT JUMP FALSE\n-------------------------------\n resnum atomnum Type TRUE/FALSE \n-------------------------------\n DEFAULT PHI FALSE\n DEFAULT THETA FALSE\n DEFAULT D FALSE\n DEFAULT RB1 FALSE\n DEFAULT RB2 FALSE\n DEFAULT RB3 FALSE\n DEFAULT RB4 FALSE\n DEFAULT RB5 FALSE\n DEFAULT RB6 FALSE\n-------------------------------\n\n\n1\n0.5\nMover name: SequenceMover, Mover type: MoverBase, Mover current tag: NoTag\n3 movers are contained in the following order:\n Mover[1]: Small\n Mover[2]: Shear\n Mover[3]: MinMover\n\nMover name: TrialMover, Mover type: MoverBase, Mover current tag: NoTag\nMover being tried: 0x40451dc200\nMoves were accepted: 0 times.\nAcceptance rate: 0\nMonteCarlo: 0x40434e1d90\n\nMover name: RepeatMover, Mover type: RepeatMover, Mover current tag: NoTag\nMover being repeated: TrialMover, nmoves: 2\n\nthon-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.655773 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nprotocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 142.844 142.844\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.moves.MonteCarlo: MC: 1 142.844 142.844 142.844 142.844 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.TrialMover: Acceptance rate: 0.5\nprotocols.moves.MonteCarlo: MC: 1 -245.18 -245.18 -245.18 -245.18 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: Small trials= 2; accepts= 0.5000; energy_drop/trial= -194.01213\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.moves.MonteCarlo: MC: 1 -303.533 -303.533 -303.533 -303.533 0 0 0 accepted score beat low\nprotocols.moves.TrialCounter: Small trials= 2; accepts= 0.5000; energy_drop/trial= -194.01213\nprotocols.moves.TrialCounter: SmallShearMinMov trials= 2; accepts= 1.0000; energy_drop/trial= -29.17653\nprotocols.moves.TrialCounter: unk trials= 1; accepts= 1.0000; energy_drop/trial= 0.00000\nprotocols.relax.ClassicRelax: Setting up default relax setting\n\nFinished Workshop5test in 0:05:13.780025", "state": "passed"}, "Workshop6test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.4734 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: 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/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/pytPyRosetta-4 2022 [Rosetta devel 2022.45.post.dev+31.HEAD.de16a55b0dc5944b8d51a811599e5006760f4f88 2022-11-15T10:18:37] 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#Packer_Task\n\nThreads to request: ALL 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831\tFALSE\tFALSE\tLEU\n832\tFALSE\tFALSE\tSER\n833\tFALSE\tFALSE\tSER\n834\tFALSE\tFALSE\tVAL\n835\tFALSE\tFALSE\tVAL\n836\tFALSE\tFALSE\tTHR\n837\tFALSE\tFALSE\tVAL\n838\tFALSE\tFALSE\tPRO\n839\tFALSE\tFALSE\tSER\n840\tFALSE\tFALSE\tSER\n841\tFALSE\tFALSE\tSER\n842\tFALSE\tFALSE\tLEU\n843\tFALSE\tFALSE\tGLY\n844\tFALSE\tFALSE\tTHR\n845\tFALSE\tFALSE\tGLN\n846\tFALSE\tFALSE\tTHR\n847\tFALSE\tFALSE\tTYR\n848\tFALSE\tFALSE\tILE\n849\tFALSE\tFALSE\t\n850\tFALSE\tFALSE\tASN\n851\tFALSE\tFALSE\tVAL\n852\tFALSE\tFALSE\tASN\n853\tFALSE\tFALSE\tHIS,HIS_D\n854\tFALSE\tFALSE\tLYS\n855\tFALSE\tFALSE\tPRO\n856\tFALSE\tFALSE\tSER\n857\tFALSE\tFALSE\tASN\n858\tFALSE\tFALSE\tTHR\n859\tFALSE\tFALSE\tLYS\n860\tFALSE\tFALSE\tVAL\n861\tFALSE\tFALSE\tASP\n862\tFALSE\tFALSE\tLYS\n863\tFALSE\tFALSE\tARG\n864\tFALSE\tFALSE\tVAL\n865\tFALSE\tFALSE\tGLU\n866\tFALSE\tFALSE\tPRO\n867\tFALSE\tFALSE\tLYS\n868\tFALSE\tFALSE\tSER:CtermProteinFull\nhon-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.647556 seconds to load from binary\ncore.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 9 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.import_pose.import_pose: File '../test/data/workshops/1YY8.clean.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 18\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 214\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 452\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 648\ncore.conformation.Conformation: Found disulfide between residues 23 88\ncore.conformation.Conformation: 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.Conformati\non: 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.pack.pack_rotamers: built 85 rotamers at 4 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 16 rotamers at 1 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph\n\nFinished Workshop6test in 0:03:21.432810", "state": "passed"}, "Workshop7test": {"log": "core.init: Checking for fconfig files in pwd and ./rosetta/flags \ncore.init: Rosetta version: 2022.45.post.dev+31.HEAD.de16a55b0dc de16a55b0dc5944b8d51a811599e5006760f4f88 git@github.com:CyrusBiotechnology/rosetta-main.git 2022-11-15T10:18:37\ncore.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\ncore.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 6.39738 seconds.\ncore.import_pose.import_pose: File '../test/data/workshops/complex.start.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 246\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 247\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 247\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 259\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 272\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 286\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 288\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 321\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 321\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 321\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 334\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 335\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 335\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 335\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 338\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 338\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 338\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 348\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 359\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 359\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 359\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 360\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 371\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 371\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 371\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 372\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 372\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 372\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 381\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 381\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 381\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 383\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 392\ncore.conformation.Conformation: Found disulfide between residues 7 137\ncore.conformation.Conformation: current variant for 7 CYS\ncore.conformation.Conformation: current variant for 137 CYS\ncore.conformation.Conformation: current variant for 7 CYD\ncore.conformation.Conformation: current variant for 137 CYD\ncore.conformation.Conformation: Found disulfide between residues 262 309\ncore.conformation.Conformation: current variant for 262 CYS\ncore.conformation.Conformation: current variant for 309 CYS\ncore.conformation.Conformation: current variant for 262 CYD\ncore.conformation.Conformation: current variant for 309 CYD\ncore.conformation.Conformation: Found disulfide between residues 25 41\ncore.conformation.Conformation: current variant for 25 CYS\ncore.conformation.Conformation: current variant for 41 CYS\ncore.conformation.Conformation: current variant for 25 CYD\ncore.conformation.Conformation: current variant for 41 CYD\ncore.conformation.Conformation: Found disulfide between residues 109 210\ncore.conformation.Conformation: current variant for 109 CYS\ncore.conformation.Conformation: current variant for 210 CYS\ncore.conformation.Conformation: current variant for 109 CYD\ncore.conformation.Conformation: current variant for 210 CYD\ncore.conformation.Conformation: Found disulfide between residues 116 183\ncore.conformation.Conformation: current variant for 116 CYS\ncore.conformation.Conformation: current variant for 183 CYS\ncore.conformation.Conformation: current variant for 116 CYD\ncore.conformation.Conformation: current variant for 183 CYD\ncore.conformation.Conformation: Found disulfide between residues 356 361\ncore.conformation.Conformation: current variant for 356 CYS\ncore.conformation.Conformation: current variant for 361 CYS\ncore.conformation.Conformation: current variant for 356 CYD\ncore.conformation.Conformation: current variant for 361 CYD\ncore.conformation.Conformation: Found disulfide between residues 148 162\ncore.conformation.Conformation: current variant for 148 CYS\ncore.conformation.Conformation: current variant for 162 CYS\ncore.conformation.Conformation: current variant for 148 CYD\ncore.conformation.Conformation: current variant for 162 CYD\ncore.conformation.Conformation: Found disulfide between residues 173 197\ncore.conformation.Conformation: current variant for 173 CYS\ncore.conformation.Conformation: current variant for 197 CYS\ncore.conformation.Conformation: current variant for 173 CYD\ncore.conformation.Conformation: current variant for 197 CYD\ncore.pack.pack_missing_sidechains: packing residue number 246 because of missing atom number 8 atom name CD1\ncore.pack.pack_missing_sidechains: packing residue number 247 because of missing atom number 6 atom name OG1\ncore.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 272 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 286 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 288 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 321 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 334 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 335 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 338 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 348 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 359 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 360 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 371 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 372 because of missing atom number 6 atom name CG \ncore.pack.pack_missing_sidechains: packing residue number 381 because of missing atom number 7 atom name CD \ncore.pack.pack_missing_sidechains: packing residue number 383 because of missing atom number 6 atom name CG \ncore.pack.task: Packer task: initialize from command line() \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\ncore.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\ncore.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-aarch64-with-glibc2.27/clang-6.0.0/python-3.9/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\ncore.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.647792 seconds to load from binary\ncore.pack.pack_rotamers: built 209 rotamers at 17 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\nbasic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\nprotocols.docking.DockingInitialPerturbation: Sliding Pose components together into contact\ncore.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types\ncore.chemical.GlobalResidueTypeSet: Total time to initialize 0.195936 seconds.\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.46\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.3\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.04\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.04\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.08\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.26\ncore.import_pose.import_pose: File '../test/data/workshops/complex.high.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: Found disulfide between residues 7 137\ncore.conformation.Conformation: current variant for 7 CYS\ncore.conformation.Conformation: current variant for 137 CYS\ncore.conformation.Conformation: current variant for 7 CYD\ncore.conformation.Conformation: current variant for 137 CYD\ncore.conformation.Conformation: Found disulfide between residues 25 41\ncore.conformation.Conformation: current variant for 25 CYS\ncore.conformation.Conformation: current variant for 41 CYS\ncore.conformation.Conformation: current variant for 25 CYD\ncore.conformation.Conformation: current variant for 41 CYD\ncore.conformation.Conformation: Found disulfide between residues 109 210\ncore.conformation.Conformation: current variant for 109 CYS\ncore.conformation.Conformation: current variant for 210 CYS\ncore.conformation.Conformation: current variant for 109 CYD\ncore.conformation.Conformation: current variant for 210 CYD\ncore.conformation.Conformation: Found disulfide between residues 116 183\ncore.conformation.Conformation: current variant for 116 CYS\ncore.conformation.Conformation: current variant for 183 CYS\ncore.conformation.Conformation: current variant for 116 CYD\ncore.conformation.Conformation: current variant for 183 CYD\ncore.conformation.Conformation: Found disulfide between residues 148 162\ncore.conformation.Conformation: current variant for 148 CYS\ncore.conformation.Conformation: current variant for 162 CYS\ncore.conformation.Conformation: current variant for 148 CYD\ncore.conformation.Conformation: current variant for 162 CYD\ncore.conformation.Conformation: Found disulfide between residues 173 197\ncore.conformation.Conformation: current variant for 173 CYS\ncore.conformation.Conformation: current variant for 197 CYS\ncore.conformation.Conformation: current variant for 173 CYD\ncore.conformation.Conformation: current variant for 197 CYD\ncore.conformation.Conformation: Found disulfide between residues 262 309\ncore.conformation.Conformation: current variant for 262 CYS\ncore.conformation.Conformation: current variant for 309 CYS\ncore.conformation.Conformation: current variant for 262 CYD\ncore.conformation.Conformation: current variant for 309 CYD\ncore.conformation.Conformation: Found disulfide between residues 356 361\ncore.conformation.Conformation: current variant for 356 CYS\ncore.conformation.Conformation: current variant for 361 CYS\ncore.conformation.Conformation: current variant for 356 CYD\ncore.conformation.Conformation: current variant for 361 CYD\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.567\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.05\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.5103\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.645\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.45927\nprotocols.docking.DockingLowRes: Rotation magnitude: 3.2805\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.413343\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.95245\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.372009\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.65721\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.334808\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.39148\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.02\nprotocols.docking.DockingLowRes: Translation magnitude: 0.301327\nprotocols.docking.DockingLowRes: Rotation magnitude: 2.15234\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: Translation magnitude: 0.271194\nprotocols.docking.DockingLowRes: Rotation magnitude: 1.9371\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0\nprotocols.docking.DockingLowRes: in DockingLowRes.apply\nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: /// Docking Low Res Protocol ///\nprotocols.docking.DockingLowRes: /// ///\nprotocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 ///\nprotocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 ///\nprotocols.docking.DockingLowRes: /// Scorefunction: ///\nprotocols.docking.DockingLowRes: ScoreFunction::show():\nweights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)\nenergy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: mhc_epitope_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: netcharge_setup_files: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT\nanalytic_etable_evaluation: 1\nEnergyMethodOptions::show: method_weights: free_res\nEnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: covalent_labeling_fa_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hrf_dynamics_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: depc_ms_input: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_hybrid: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: count_pair_full: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_wat_penalty: 1.221\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_ref_seq_length_: 9\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_term_length_: 3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_scorecut_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_aa_matrix_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_list_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: nmer_svm_rank_: \nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_bonus_ramping_function_: \"quadratic\"\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: hbnet_max_network_size_: 0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: target_clash_pdb_:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_prefix_: traj\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_gz_: FALSE\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: dump_trajectory_stride_: 1\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:\nprotocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none\nprotocols.docking.DockingLowRes: HBondOptions::show: hb_max_energy: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true\nprotocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true\nprotocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true\nprotocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false\nprotocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params\nprotocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75\nprotocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357\nprotocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true\nprotocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1\nprotocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false \nprotocols.docking.DockingLowRes: HbondOptions::show: mphbond: false\nprotocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0\nprotocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson\nprotocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25\nprotocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5\nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: \nprotocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////\nprotocols.docking.DockingLowRes: ::::::::::::::::::Centroid Adaptive:::::::::::::::::::\nprotocols.docking.DockingLowRes: Translation magnitude: 0.7\nprotocols.docking.DockingLowRes: Rotation magnitude: 5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Accepted\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Acceptance rate is: 0.06\nprotocols.docking.DockingLowRes: Translation magnitude: 0.63\nprotocols.docking.DockingLowRes: Rotation magnitude: 4.5\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.DockingLowRes: Rigid Body Perturbation Rejected\nprotocols.docking.Dock