core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: snugdock.linuxgccrelease -s /home/jeneric/work/shared/hvy_cha.pdb -partners LH_A -out:file:scorefile score_out_snugdock.sc -out:path:pdb models_path_out/ -out:pdb_gz -nstruct 1 -constraints:cst_weight 1.0 -constraints:cst_fa_weight 1.0 -spin -dock_pert 3 8 -h3_filter false -kic_rama2b -loops:ramp_fa_rep -loops:ramp_rama -kic_omega_sampling -allow_omega_move true -loops:refine_outer_cycles 1 -loops:max_inner_cycles 1 -ex1 -ex2aro -input_ab_scheme Chothia_Scheme core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-751928344 seed_offset=0 real_seed=-751928344 core.init.random: RandomGenerator:init: Normal mode, seed=-751928344 RG_type=mt19937 core.init: Resolved executable path: /home/jeneric/Desktop/jen/abcelex/rosetta_src_2017.08.59291_bundle/main/source/build/src/release/linux/4.8/64/x86/gcc/6.2/default/snugdock.default.linuxgccrelease core.init: Looking for database based on location of executable: /home/jeneric/Desktop/jen/abcelex/rosetta_src_2017.08.59291_bundle/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /home/jeneric/work/shared/hvy_cha.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /home/jeneric/work/shared/hvy_cha.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 544 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.27883 seconds. core.import_pose.import_pose: File '/home/jeneric/work/shared/hvy_cha.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 63 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 63 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 63 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 65 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 65 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 65 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 65 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 65 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 205 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 205 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 205 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 205 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 205 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 236 core.conformation.Conformation: Found disulfide between residues 22 96 core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 96 CYS core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: Found disulfide between residues 144 213 core.conformation.Conformation: current variant for 144 CYS core.conformation.Conformation: current variant for 213 CYS core.conformation.Conformation: current variant for 144 CYD core.conformation.Conformation: current variant for 213 CYD core.pack.pack_missing_sidechains: packing residue number 63 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 8 atom name CE core.pack.pack_missing_sidechains: packing residue number 151 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 205 because of missing atom number 7 atom name CD core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/jeneric/Desktop/jen/abcelex/rosetta_src_2017.08.59291_bundle/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.065714 seconds to load from binary core.pack.pack_rotamers: built 83 rotamers at 5 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 3544 bytes protocols.antibody.SnugDockProtocol: Beginning apply function of SnugDockProtocol. protocols.antibody.SnugDockProtocol: Setting up data for SnugDockProtocol. basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: Could not setup Vl Vh Packing angle for camelid antibody antibody.AntibodyInfo: AC Detecting Camelid CDR H3 Stem Type antibody.AntibodyInfo: AC Finished Detecting Camelid CDR H3 Stem Type: NEUTRAL protocols.loops.util: checking peptide bond geometry: protocols.loops.util: checking peptide bond geometry: protocols.loops.util: checking peptide bond geometry: antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 protocols.docking.DockingInitialPerturbation: Reading options... core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 protocols.antibody.SnugDockProtocol: SnugDockProtocol has been configured to operate on an Antibody-Antigen complex with the following information: protocols.antibody.SnugDockProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: /// Rosetta Antibody Info /// protocols.antibody.SnugDockProtocol: /// /// protocols.antibody.SnugDockProtocol: /// Antibody Type: Camelid Antibody protocols.antibody.SnugDockProtocol: /// Light Chain Type: unknown protocols.antibody.SnugDockProtocol: /// Predict H3 Cterminus Base: NEUTRAL protocols.antibody.SnugDockProtocol: /// protocols.antibody.SnugDockProtocol: /// H1 info: protocols.antibody.SnugDockProtocol: /// length: 10 protocols.antibody.SnugDockProtocol: /// sequence: GYTFTNYYMY protocols.antibody.SnugDockProtocol: /// north_cluster: H1-13-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 26 stop: 35 cut: 31 size: 10 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// H2 info: protocols.antibody.SnugDockProtocol: /// length: 17 protocols.antibody.SnugDockProtocol: /// sequence: GINPSNGGTNFNEKFKN protocols.antibody.SnugDockProtocol: /// north_cluster: H2-10-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 50 stop: 66 cut: 58 size: 17 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// H3 info: protocols.antibody.SnugDockProtocol: /// length: 11 protocols.antibody.SnugDockProtocol: /// sequence: RDYRFDMGFDY protocols.antibody.SnugDockProtocol: /// north_cluster: H3-13-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 99 stop: 109 cut: 100 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: Setting the input structure's FoldTree for Antibody-Antigen docking. protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job hvy_cha_0001Chains are not named correctly or are not in the expected order protocols.jd2.JobDistributor: protocols.jd2.JobDistributor: hvy_cha_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 2 seconds