core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373 core.init: command: docking_prepack_protocol.static.linuxgccrelease -in:file:s 3sn6_pdbtm.pdb -score:weights mpframework_docking_fa_2015.wts -mp:setup:spanfiles 3sn6_pdbtm.span -mp:scoring:hbond -packing:pack_missing_sidechains 0 -partners R_ABGN -nstruct 1 -out:prefix mpdock_prepack/ core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-174754738 seed_offset=0 real_seed=-174754738 core.init.random: RandomGenerator:init: Normal mode, seed=-174754738 RG_type=mt19937 core.init: Resolved executable path: /home/hildilab/dev/ext/rosetta/2018.09/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/docking_prepack_protocol.static.linuxgccrelease core.init: Looking for database based on location of executable: /home/hildilab/dev/ext/rosetta/2018.09/main/database/ core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.ScoreFunctionFactory: SCOREFUNCTION: mpframework_docking_fa_2015.wts core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. core.scoring.etable: Using alternate parameters: LK_DGFREE in MembEtable construction. core.scoring.etable: Using alternate parameters: MEMB_LK_DGFREE in MembEtable construction. core.scoring.etable: Using alternate parameters: LK_DGREFCE in MembEtable construction. core.scoring.etable: Using alternate parameters: MEMB_LK_DGREFCE in MembEtable construction. core.scoring.etable: Starting membrane specific energy table calculation core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating membrane specific energy tables. basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_Menv_smooth_log.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 3sn6_pdbtm.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 3sn6_pdbtm.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 603 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.39 seconds. core.import_pose.import_pose: File '3sn6_pdbtm.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 68 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 68 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 68 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 68 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 69 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 69 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE1 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE3 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ2 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ3 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CH2 on residue TRP 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 72 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 72 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 72 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 72 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 72 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 72 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 146 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 146 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 146 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 146 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 146 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 146 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 160 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 160 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 160 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 161 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PHE 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue PHE 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue PHE 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE2 on residue PHE 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue PHE 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 210 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 212 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 212 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 212 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 212 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 212 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 213 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 213 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 213 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 213 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LEU 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue LEU 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue LEU 215 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 244 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 244 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 244 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LEU 245 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue LEU 245 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue LEU 245 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 247 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 249 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 249 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 249 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 249 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 276 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 276 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 276 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 276 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 276 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 276 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 284 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 300 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 300 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 300 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 300 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 311 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 311 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 311 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 311 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 334 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 335 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 342 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 342 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 342 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 366 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 366 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 366 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 366 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 384 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 384 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 384 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 387 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 387 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 387 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 436 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 436 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 436 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 437 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 437 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 437 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 439 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 439 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 442 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 442 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 442 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 449 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 449 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 449 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 449 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 449 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 449 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 462 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 462 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 462 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 462 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 486 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 486 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 486 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 539 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 539 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 539 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 539 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 561 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 561 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 561 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 561 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 608 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 608 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN:NtermProteinFull 634 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN:NtermProteinFull 634 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN:NtermProteinFull 634 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN:NtermProteinFull 634 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 675 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 675 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 675 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 675 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 675 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 675 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 762 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 762 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 762 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 762 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 762 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 762 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 763 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 763 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 763 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 763 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 805 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 805 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 805 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 805 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG:CtermProteinFull 1031 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SER 1143 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 1144 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 1144 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 1159 core.conformation.Conformation: Found disulfide between residues 77 159 core.conformation.Conformation: current variant for 77 CYS core.conformation.Conformation: current variant for 159 CYS core.conformation.Conformation: current variant for 77 CYD core.conformation.Conformation: current variant for 159 CYD core.conformation.Conformation: Found disulfide between residues 152 158 core.conformation.Conformation: current variant for 152 CYS core.conformation.Conformation: current variant for 158 CYS core.conformation.Conformation: current variant for 152 CYD core.conformation.Conformation: current variant for 158 CYD core.conformation.Conformation: Found disulfide between residues 1053 1127 core.conformation.Conformation: current variant for 1053 CYS core.conformation.Conformation: current variant for 1127 CYS core.conformation.Conformation: current variant for 1053 CYD core.conformation.Conformation: current variant for 1127 CYD core.conformation.Conformation: Found disulfide between residues 1130 1138 core.conformation.Conformation: current variant for 1130 CYS core.conformation.Conformation: current variant for 1138 CYS core.conformation.Conformation: current variant for 1130 CYD core.conformation.Conformation: current variant for 1138 CYD protocols.membrane.AddMembraneMover: ===================================================================== protocols.membrane.AddMembraneMover: || WELCOME TO THE WORLD OF MEMBRANE PROTEINS... || protocols.membrane.AddMembraneMover: ===================================================================== protocols.membrane.AddMembraneMover: No membrane residue was found protocols.membrane.AddMembraneMover: Adding a new membrane residue to the pose protocols.membrane.AddMembraneMover: Adding a membrane residue representing the position of the membrane after residue 1159 protocols.membrane.AddMembraneMover: Edge Jump Jump # 1160--0001 005 0001--0284 0001--0285 001 0285--0633 0001--0634 002 0634--0973 0001--0974 003 0974--1031 0001--1032 004 1032--1159 core.conformation.membrane.SpanningTopology: Filling membrane spanning topology from spanfile 3sn6_pdbtm.span core.conformation.membrane.SpanningTopology: nres: 1160 core.conformation.membrane.SpanningTopology: nres_topo: 284 core.conformation.membrane.SpanningTopology: total residues in spanfile: 284 core.conformation.membrane.SpanningTopology: Pose is in pose numbering scheme. core.conformation.membrane.SpanningTopology: Total # of TM spans: 7 core.conformation.membrane.SpanningTopology: Number of residues in spanfile: 284 core.conformation.membrane.SpanningTopology: Span 1: start: 3, end: 29 orientation: 1 core.conformation.membrane.SpanningTopology: Span 2: start: 42, end: 67 orientation: 1 core.conformation.membrane.SpanningTopology: Span 3: start: 76, end: 101 orientation: 1 core.conformation.membrane.SpanningTopology: Span 4: start: 122, end: 146 orientation: 1 core.conformation.membrane.SpanningTopology: Span 5: start: 164, end: 189 orientation: 1 core.conformation.membrane.SpanningTopology: Span 6: start: 219, end: 243 orientation: 1 core.conformation.membrane.SpanningTopology: Span 7: start: 249, end: 271 orientation: 1 protocols.membrane.AddMembraneMover: MembraneInfo: protocols.membrane.AddMembraneMover: MembraneInfo: Information about this Membrane Protein protocols.membrane.AddMembraneMover: Membrane Residue Num: 1160 protocols.membrane.AddMembraneMover: Membrane Fold Tree Jump: 5 protocols.membrane.AddMembraneMover: Membrane Thickness: 15 protocols.membrane.AddMembraneMover: Membrane core: 15 protocols.membrane.AddMembraneMover: Membrane Steepness: 10 protocols.membrane.AddMembraneMover: Membrane Spanning Topology core.conformation.membrane.SpanningTopology: Total # of TM spans: 7 core.conformation.membrane.SpanningTopology: Number of residues in spanfile: 284 core.conformation.membrane.SpanningTopology: Span 1: start: 3, end: 29 orientation: 1 core.conformation.membrane.SpanningTopology: Span 2: start: 42, end: 67 orientation: 1 core.conformation.membrane.SpanningTopology: Span 3: start: 76, end: 101 orientation: 1 core.conformation.membrane.SpanningTopology: Span 4: start: 122, end: 146 orientation: 1 core.conformation.membrane.SpanningTopology: Span 5: start: 164, end: 189 orientation: 1 core.conformation.membrane.SpanningTopology: Span 6: start: 219, end: 243 orientation: 1 core.conformation.membrane.SpanningTopology: Span 7: start: 249, end: 271 orientation: 1 protocols.membrane.SetMembranePositionMover: Calling SetMembranePositionMover protocols.membrane.SetMembranePositionMover: Starting foldtree: Is membrane fixed? 1 protocols.membrane.SetMembranePositionMover: Edge Jump Jump # 1160--0001 005 0001--0284 0001--0285 001 0285--0633 0001--0634 002 0634--0973 0001--0974 003 0974--1031 0001--1032 004 1032--1159 protocols.membrane.SetMembranePositionMover: Final foldtree: Is membrane fixed? 1 protocols.membrane.SetMembranePositionMover: Edge Jump Jump # 1160--0001 005 0001--0284 0001--0285 001 0285--0633 0001--0634 002 0634--0973 0001--0974 003 0974--1031 0001--1032 004 1032--1159 protocols.membrane.AddMembraneMover: Final foldtree: Is membrane fixed? 1 protocols.membrane.AddMembraneMover: Edge Jump Jump # 1160--0001 005 0001--0284 0001--0285 001 0285--0633 0001--0634 002 0634--0973 0001--0974 003 0974--1031 0001--1032 004 1032--1159 protocols.membrane.util: chainid 1 chain R protocols.membrane.util: com (21.2484, 7.06581, -1.89306) protocols.membrane.util: chainid 2 chain A core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 2 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 4 to 2 protocols.membrane.util: com (16.161, -6.66752, 41.0602) protocols.membrane.util: chainid 3 chain B core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 4 to 1 core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 2 to 1 protocols.membrane.util: com (44.2798, 6.52833, 50.7413) protocols.membrane.util: chainid 4 chain G core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 4 to 1 core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 2 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 3 to 2 core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 2 to 1 protocols.membrane.util: com (53.0824, 13.161, 56.9253) protocols.membrane.util: chainid 5 chain N core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 4 to 1 core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 2 core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 3 to 2 core.conformation.Conformation: Found disulfide between residues 22 96 core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: Found disulfide between residues 99 107 core.conformation.Conformation: current variant for 99 CYD core.conformation.Conformation: current variant for 107 CYD core.conformation.Conformation: current variant for 99 CYD core.conformation.Conformation: current variant for 107 CYD protocols.membrane.util: com (19.5822, 26.5452, 62.7248) protocols.membrane.util: partners R_ABGN protocols.membrane.util: mem rsd 1160 protocols.membrane.util: anchors[1] 88 protocols.membrane.util: Edge Jump Jump # 1160--0088 001 0088--0284 0088--0465 005 0465--0633 0465--0865 002 0865--0634 0865--0973 0465--1006 003 1006--0974 1006--1031 0465--1067 004 1067--1159 1067--1032 0465--0285 0088--0001 core.conformation.membrane.MembraneInfo: Setting a new membrane jump number in MembraneInfo to 1. core.conformation.membrane.MembraneInfo: Use with caution! basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_Menv_smooth_log.txt protocols.membrane.geometry.Embedding: Constructing Embedding object from topology and pose protocols.membrane.geometry.Embedding: Computing membrane embedding from TMspans: protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 3 to 29 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 3 to 29 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 42 to 67 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 76 to 101 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 122 to 146 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 164 to 189 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 219 to 243 protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 249 to 271 protocols.membrane.geometry.Embedding: Span Embedding: protocols.membrane.geometry.EmbeddingDef: Embedding: center: (29.3595, 18.5775, 0.2875), normal: (0.246342, -0.527118, 0.813303) protocols.membrane.geometry.EmbeddingDef: Embedding: center: (28.0385, 10.28, -3.163), normal: (-0.166901, -0.454335, 0.875056) protocols.membrane.geometry.EmbeddingDef: Embedding: center: (25.768, 1.8505, 0.5895), normal: (-0.478818, -0.072278, 0.874934) protocols.membrane.geometry.EmbeddingDef: Embedding: center: (23.98, -4.6795, -3.25), normal: (0.228514, -0.054418, 0.972019) protocols.membrane.geometry.EmbeddingDef: Embedding: center: (9.4525, 0.596, -0.4655), normal: (-0.270991, 0.15619, 0.949825) protocols.membrane.geometry.EmbeddingDef: Embedding: center: (7.684, 11.1045, -4.6245), normal: (0.069577, 0.283952, 0.956311) protocols.membrane.geometry.EmbeddingDef: Embedding: center: (19.645, 16.4005, 0.6465), normal: (0.213196, -0.0374885, 0.97629) protocols.membrane.geometry.Embedding: Total Embedding: protocols.membrane.geometry.EmbeddingDef: Embedding: center: (20.5611, 7.73279, -1.42564), normal: (-0.0246318, -0.109238, 0.99371) ERROR: The SpanningTopology object in MembraneInfo is empty! ERROR:: Exit from: src/protocols/membrane/util.cc line: 1224 BACKTRACE: [0x58cb7a8] [0x24cbe8e] [0x24cc8e0] [0x24ccb83] [0x1c6e3c8] [0x35af678] [0x35b1181] [0x3653cf8] [0x410997] [0x5e11504] [0x61508d] protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job mpdock_prepack/3sn6_pdbtm_0001 File: src/protocols/membrane/util.cc:1224 [ ERROR ] UtilityExitException ERROR: The SpanningTopology object in MembraneInfo is empty! protocols.jd2.JobDistributor: [ ERROR ] protocols.jd2.JobDistributor: [ WARNING ] mpdock_prepack/3sn6_pdbtm_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3 seconds caught exception File: src/protocols/jd2/JobDistributor.cc:329 1 jobs failed; check output for error messages