In [6]: run D120_Ligand_interface.py Invalid PYROSETTA_DATABASE environment variable was specified: /home/herath/Research/PyR/rosetta_database Found rosetta database at: /home/herath/Research/PyR/database; using it.... PyRosetta 2014 [Rosetta 2014 56891:56891:6efc58f8abb54611ace5a6cdd7e69e6c970a01ef] retrieved from: (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. core.init: Rosetta version from core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/herath/Research/PyR/database core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 371 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ASP:NtermProteinFull core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 372 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ALA core.io.pdb.file_data: [ WARNING ] discarding 5 atoms at position 373 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLU core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 374 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: PHE core.io.pdb.file_data: [ WARNING ] discarding 10 atoms at position 375 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ARG core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 376 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: HIS core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 377 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ASP core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 378 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: SER core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 379 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 380 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: TYR core.io.pdb.file_data: [ WARNING ] discarding 5 atoms at position 381 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLU core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 382 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: VAL core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 383 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: HIS core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 384 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: HIS core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 385 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLN core.io.pdb.file_data: [ WARNING ] discarding 11 atoms at position 386 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: LYS core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 387 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: LEU core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 388 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: VAL core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 389 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: PHE core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 390 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: PHE core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 391 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ALA core.io.pdb.file_data: [ WARNING ] discarding 5 atoms at position 392 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLU core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 393 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ASP core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 394 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: VAL core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 395 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 396 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: SER core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 397 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ASN core.io.pdb.file_data: [ WARNING ] discarding 11 atoms at position 398 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: LYS core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 399 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 400 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ALA core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 401 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ILE core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 402 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ILE core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 403 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 404 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: LEU core.io.pdb.file_data: [ WARNING ] discarding 7 atoms at position 405 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: MET core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 406 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: VAL core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 407 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 408 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: GLY core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 409 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: VAL core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 410 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: VAL core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 411 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ILE core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 412 in file 2BG9_ChainA.clean.pdb. Best match rsd_type: ALA:CtermProteinFull core.conformation.Conformation: Found disulfide between residues 128 142 core.conformation.Conformation: current variant for 128 CYS core.conformation.Conformation: current variant for 142 CYS core.conformation.Conformation: current variant for 128 CYD core.conformation.Conformation: current variant for 142 CYD core.conformation.Conformation: Found disulfide between residues 192 193 core.conformation.Conformation: current variant for 192 CYS core.conformation.Conformation: current variant for 193 CYS core.conformation.Conformation: current variant for 192 CYD core.conformation.Conformation: current variant for 193 CYD core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 protocols.docking.DockMCMProtocol: in DockMCMProtocol.apply protocols.docking.DockMCMProtocol: Using the DockingTaskFactory. protocols.docking.DockMCMCycle: Setting up defaults for DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockMCMCycle: /// Dockable Jumps: 1 /// protocols.docking.DockMCMCycle: /// Translation: 0.1 /// protocols.docking.DockMCMCycle: /// Rotation: 5 /// protocols.docking.DockMCMCycle: /// Scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.8) (fa_rep 0.4) (fa_sol 0.6) (fa_elec 0.25) (pro_close 1) (fa_pair 0.8) (hbond_sr_bb 2) (hbond_lr_bb 2) (hbond_bb_sc 2) (hbond_sc 2) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (atom_pair_constraint 1) (coordinate_constraint 1) (angle_constraint 1) (dihedral_constraint 1) (omega 0.5) (fa_dun 0.4) (p_aa_pp 0.5) (ref 1) (chainbreak 1) energy_method_options: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.05 0.09 -0.65 -0.27 1.88 -0.55 1.17 -0.73 -0.42 -0.66 -0.29 -0.76 -0.33 -0.29 -0.77 0 -0.57 -0.57 2.88 0.81 EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: include_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: sp2_elec_params protocols.docking.DockMCMCycle: HBondOptions::show: use_incorrect_deriv_: false protocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.8) (fa_rep 0.44) (fa_sol 0.75) (fa_intra_rep 0.004) (fa_elec 0.7) (pro_close 1) (hbond_sr_bb 1.17) (hbond_lr_bb 1.17) (hbond_bb_sc 1.17) (hbond_sc 1.1) (dslf_fa13 1) (rama 0.2) (omega 0.5) (fa_dun 0.56) (p_aa_pp 0.32) (ref 1) energy_method_options: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.592942 0.354993 -1.28682 -1.55374 0.43057 0.140526 0.357498 0.831803 -0.287374 0.602328 0.158677 -0.94198 -0.219285 -1.17797 -0.14916 0.176583 0.16454 0.744844 0.92933 0.131696 EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: HBondOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: include_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: HBondOptions::show: params_database_tag_: sp2_elec_params protocols.docking.DockMCMCycle: HBondOptions::show: use_incorrect_deriv_: false protocols.docking.DockMCMCycle: HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.pack_rotamers: IG: 480 bytes protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.pack_rotamers: IG: 480 bytes protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.pack_rotamers: IG: 480 bytes protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.pack_rotamers: IG: 480 bytes protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.pack_rotamers: IG: 480 bytes protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.pack_rotamers: IG: 480 bytes protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!! protocols.geometry.RB_geometry: calling centroids_by_jump... core.pack.task: Packer task: initialize from command line() In [7]: