[vispd4:native]> ~/rosetta/bin/snugdock.linuxgccrelease @snugdock.flags core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: /home/amwoll/rosetta/bin/snugdock.linuxgccrelease @snugdock.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=935904843 seed_offset=0 real_seed=935904843 core.init.random: RandomGenerator:init: Normal mode, seed=935904843 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /home/amwoll/rosetta/database protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed complex.prepack.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB complex.prepack.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 544 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.386737 seconds. core.import_pose.import_pose: File 'complex.prepack.pdb' automatically determined to be of type PDB 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: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: ARHGAYYSNAFDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 protocols.loops.util: checking peptide bond geometry: protocols.loops.util: checking peptide bond geometry: protocols.loops.util: checking peptide bond geometry: 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 antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/hbonds/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/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt 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 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 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 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: Regular Antibody protocols.antibody.SnugDockProtocol: /// Light Chain Type: unknown protocols.antibody.SnugDockProtocol: /// Predict H3 Cterminus Base: KINKED protocols.antibody.SnugDockProtocol: /// protocols.antibody.SnugDockProtocol: /// H1 info: protocols.antibody.SnugDockProtocol: /// length: 10 protocols.antibody.SnugDockProtocol: /// sequence: GYTFTDYTIH protocols.antibody.SnugDockProtocol: /// north_cluster: H1-13-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 137 stop: 146 cut: 142 size: 10 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// H2 info: protocols.antibody.SnugDockProtocol: /// length: 17 protocols.antibody.SnugDockProtocol: /// sequence: WIYPLRGSINYNEKFKD protocols.antibody.SnugDockProtocol: /// north_cluster: H2-10-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 161 stop: 177 cut: 169 size: 17 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// H3 info: protocols.antibody.SnugDockProtocol: /// length: 11 protocols.antibody.SnugDockProtocol: /// sequence: HGAYYSNAFDY protocols.antibody.SnugDockProtocol: /// north_cluster: H3-13-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 210 stop: 220 cut: 211 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// L1 info: protocols.antibody.SnugDockProtocol: /// length: 15 protocols.antibody.SnugDockProtocol: /// sequence: RASESVDNDGIRFMH protocols.antibody.SnugDockProtocol: /// north_cluster: L1-15-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 24 stop: 38 cut: 31 size: 15 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// L2 info: protocols.antibody.SnugDockProtocol: /// length: 7 protocols.antibody.SnugDockProtocol: /// sequence: RASNLES protocols.antibody.SnugDockProtocol: /// north_cluster: L2-8-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 54 stop: 60 cut: 57 size: 7 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: protocols.antibody.SnugDockProtocol: /// L3 info: protocols.antibody.SnugDockProtocol: /// length: 9 protocols.antibody.SnugDockProtocol: /// sequence: QQSNKDPYT protocols.antibody.SnugDockProtocol: /// north_cluster: L3-9-cis7-1 protocols.antibody.SnugDockProtocol: /// loop_info: LOOP start: 93 stop: 101 cut: 97 size: 9 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. antibody.util: Automatically setting kink constraint! protocols.antibody.SnugDockProtocol: Beginning application of DockingProtocol. protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor! protocols.docking.DockingProtocol: Ensemble 1: ensemble_antibody.list protocols.moves.DockingEnsemble: Loading Ensemble core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antibody/m2419_mab_r10_0001.pdb.ppk' automatically determined to be of type PDB core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antibody/m2419_mab_r1_0001.pdb.ppk' automatically determined to be of type PDB core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antibody/m2419_mab_r10_0001.pdb.ppk' automatically determined to be of type PDB core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antibody/m2419_mab_r1_0001.pdb.ppk' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: For ResidueTypeSet centroid there is no shadow_list.txt file to list known PDB ids. core.chemical.GlobalResidueTypeSet: This will turn off PDB component loading for ResidueTypeSet centroid core.chemical.GlobalResidueTypeSet: Expected file: /home/amwoll/rosetta/database/chemical/residue_type_sets/centroid/shadow_list.txt core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.017595 seconds. protocols.moves.DockingEnsemble: ensemble summary: start_res_ 1 end_res_ 231 conf_size_ 231 ensemble_size_ 2 protocols.docking.DockingProtocol: Ensemble 2: ensemble_antigen.list protocols.moves.DockingEnsemble: Loading Ensemble core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antigen/mut2B_0001.pdb.ppk' automatically determined to be of type PDB core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antigen/mut2B_0002.pdb.ppk' automatically determined to be of type PDB core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antigen/mut2B_0001.pdb.ppk' automatically determined to be of type PDB core.import_pose.import_pose: File '/scratch/amwoll/2419/runs/docking/snugdock/native/antigen/mut2B_0002.pdb.ppk' automatically determined to be of type PDB protocols.moves.DockingEnsemble: ensemble summary: start_res_ 232 end_res_ 642 conf_size_ 411 ensemble_size_ 2 protocols.docking.DockingProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: /// /// protocols.docking.DockingProtocol: /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: /// High Resolution Filter: on /// protocols.docking.DockingProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: FOLD_TREE EDGE 1 111 -1 EDGE 111 112 2 EDGE 112 148 -1 EDGE 148 231 -1 EDGE 148 468 1 EDGE 468 369 -1 EDGE 369 368 3 EDGE 368 232 -1 EDGE 468 505 -1 EDGE 505 506 4 EDGE 506 642 -1 protocols.docking.DockingInitialPerturbation: sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: sliding into contact protocols.docking.DockingInitialPerturbation: Moving away protocols.docking.DockingInitialPerturbation: Moving together protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.837895 -0.545167 -0.0269342 -0.480714 -0.713661 -0.509512 0.258547 0.439865 -0.860042 -22.8183 14.4366 20.6715 protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.837895 -0.545167 -0.0269342 -0.480714 -0.713661 -0.509512 0.258547 0.439865 -0.860042 -22.0914 14.0179 20.1271 protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.837895 -0.545167 -0.0269342 -0.480714 -0.713661 -0.509512 0.258547 0.439865 -0.860042 -22.0914 14.0179 20.1271 protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.837895 -0.545167 -0.0269342 -0.480714 -0.713661 -0.509512 0.258547 0.439865 -0.860042 -22.8183 14.4366 20.6715 protocols.docking.DockingProtocol: finished initial perturbation protocols.docking.DockingLowRes: in DockingLowRes.apply protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: /// /// protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: /// Scorefunction: /// protocols.docking.DockingLowRes: ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (dock_ens_conf 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: sp2_elec_params protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: protocols.docking.DockingLowRes: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: /// Ensemble 1: on /// protocols.docking.DockingLowRes: /// Ensemble 2: on /// protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive::::::::::::::::::: Segmentation fault (core dumped)