core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: /home/chao/rosetta/main/source/bin/antibody_H3.linuxclangrelease @abH3.flags -s grafting/model-0.relaxed.pdb -nstruct 1000 -antibody:auto_generate_kink_constraint -antibody:all_atom_mode_kink_constraint -multiple_processes_writing_to_one_directory -out:file:scorefile H3_modeling_scores.fasc -out:path:pdb H3_modeling core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-333216494 seed_offset=0 real_seed=-333216494 core.init.random: RandomGenerator:init: Normal mode, seed=-333216494 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /home/chao/rosetta/main/database protocols.antibody.AntibodyModelerProtocol: Setting Up defaults.......... protocols.antibody.AntibodyModelerProtocol: Start Reading and Setting Options ... protocols.antibody.AntibodyModelerProtocol: Finish Reading and Setting Options !!! 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 basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine 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 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 protocols.antibody: //////////////////////////////////////////////////////////////////////////////// protocols.antibody: /// protocols.antibody: /// Rosetta 3 Antibody Modeler /// protocols.antibody: /// /// protocols.antibody: /// protocols.antibody: /// ****** model_h3 : 1 protocols.antibody: /// h3_perturb_type = 'perturb_kic' protocols.antibody: /// cter_insert = 0 protocols.antibody: /// h3_filter = 0 protocols.antibody: /// protocols.antibody: /// ****** snugfit : 1 protocols.antibody: /// LH_repulsive_ramp = 1 protocols.antibody: /// protocols.antibody: /// ****** refine_h3 : 1 protocols.antibody: /// h3_refine_type = 'refine_kic' protocols.antibody: /// h3_filter = 0 protocols.antibody: /// h3_filter_tolerance = 5 protocols.antibody: /// protocols.antibody: //////////////////////////////////////////////////////////////////////////////// protocols.antibody: protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed grafting/model-0.relaxed.pdb nstruct indices 1 - 1000 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB grafting/model-0.relaxed.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 544 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.34434 seconds. core.import_pose.import_pose: File 'grafting/model-0.relaxed.pdb' automatically determined to be of type PDB core.conformation.Conformation: Found disulfide between residues 22 95 core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 95 CYS core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 95 CYD core.conformation.Conformation: Found disulfide between residues 138 203 core.conformation.Conformation: current variant for 138 CYS core.conformation.Conformation: current variant for 203 CYS core.conformation.Conformation: current variant for 138 CYD core.conformation.Conformation: current variant for 203 CYD protocols.antibody.AntibodyModelerProtocol: Danger Will Robinson! Native is an impostor! protocols.antibody.AntibodyModelerProtocol: 'native_pose' is just a copy of the 'input_pose' protocols.antibody.AntibodyModelerProtocol: since you didn't sepcifiy the native pdb name 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: ARERDYRLDYW 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: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT 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 protocols.antibody.AntibodyModelerProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.AntibodyModelerProtocol: /// Rosetta Antibody Info /// protocols.antibody.AntibodyModelerProtocol: /// /// protocols.antibody.AntibodyModelerProtocol: /// Antibody Type: Regular Antibody protocols.antibody.AntibodyModelerProtocol: /// Light Chain Type: unknown protocols.antibody.AntibodyModelerProtocol: /// Predict H3 Cterminus Base: KINKED protocols.antibody.AntibodyModelerProtocol: /// protocols.antibody.AntibodyModelerProtocol: /// H1 info: protocols.antibody.AntibodyModelerProtocol: /// length: 10 protocols.antibody.AntibodyModelerProtocol: /// sequence: GFSLTGYGVN protocols.antibody.AntibodyModelerProtocol: /// north_cluster: H1-13-2 protocols.antibody.AntibodyModelerProtocol: /// loop_info: LOOP start: 26 stop: 35 cut: 31 size: 10 skip rate: 0 extended?: False protocols.antibody.AntibodyModelerProtocol: protocols.antibody.AntibodyModelerProtocol: /// H2 info: protocols.antibody.AntibodyModelerProtocol: /// length: 16 protocols.antibody.AntibodyModelerProtocol: /// sequence: MIWGDGNTDYNSALKS protocols.antibody.AntibodyModelerProtocol: /// north_cluster: H2-9-1 protocols.antibody.AntibodyModelerProtocol: /// loop_info: LOOP start: 50 stop: 65 cut: 58 size: 16 skip rate: 0 extended?: False protocols.antibody.AntibodyModelerProtocol: protocols.antibody.AntibodyModelerProtocol: /// H3 info: protocols.antibody.AntibodyModelerProtocol: /// length: 8 protocols.antibody.AntibodyModelerProtocol: /// sequence: ERDYRLDY protocols.antibody.AntibodyModelerProtocol: /// north_cluster: H3-10-1 protocols.antibody.AntibodyModelerProtocol: /// loop_info: LOOP start: 98 stop: 105 cut: 99 size: 8 skip rate: 0 extended?: False protocols.antibody.AntibodyModelerProtocol: protocols.antibody.AntibodyModelerProtocol: /// L1 info: protocols.antibody.AntibodyModelerProtocol: /// length: 11 protocols.antibody.AntibodyModelerProtocol: /// sequence: RASGNIHNYLA protocols.antibody.AntibodyModelerProtocol: /// north_cluster: L1-11-2 protocols.antibody.AntibodyModelerProtocol: /// loop_info: LOOP start: 139 stop: 149 cut: 144 size: 11 skip rate: 0 extended?: False protocols.antibody.AntibodyModelerProtocol: protocols.antibody.AntibodyModelerProtocol: /// L2 info: protocols.antibody.AntibodyModelerProtocol: /// length: 7 protocols.antibody.AntibodyModelerProtocol: /// sequence: YTTTLAD protocols.antibody.AntibodyModelerProtocol: /// north_cluster: L2-8-2 protocols.antibody.AntibodyModelerProtocol: /// loop_info: LOOP start: 165 stop: 171 cut: 168 size: 7 skip rate: 0 extended?: False protocols.antibody.AntibodyModelerProtocol: protocols.antibody.AntibodyModelerProtocol: /// L3 info: protocols.antibody.AntibodyModelerProtocol: /// length: 9 protocols.antibody.AntibodyModelerProtocol: /// sequence: QHFWSTPRT protocols.antibody.AntibodyModelerProtocol: /// north_cluster: L3-9-cis7-2 protocols.antibody.AntibodyModelerProtocol: /// loop_info: LOOP start: 204 stop: 212 cut: 208 size: 9 skip rate: 0 extended?: False protocols.antibody.AntibodyModelerProtocol: protocols.antibody.AntibodyModelerProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody.AntibodyModelerProtocol: 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/chao/rosetta/main/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 0.014943 seconds. protocols.antibody.AntibodyModelerProtocol: Centroid cst_weight: 0 protocols.antibody.ModelCDRH3: Applying CDR H3 modeler protocols.antibody.ModelCDRH3: Extend the H3 loop ........... protocols.loops.loops_main: USING A DEPRECATED FUNCTION!( loops::set_extended_torsions(...) ) core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 99-1, 99-2, 99-3, 100-1! core.kinematics.AtomTree: DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: Unable to set torsion angle in atom_tree: TorsionID 99 BB 2 core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 99-2, 99-3, 100-1, 100-2! core.kinematics.AtomTree: DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: Unable to set torsion angle in atom_tree: TorsionID 99 BB 3 core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 99-3, 100-1, 100-2, 100-3! core.kinematics.AtomTree: DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: Unable to set torsion angle in atom_tree: TorsionID 100 BB 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: ALL_LOOPS:LOOP begin end cut skip_rate extended protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: LOOP start: 96 stop: 105 cut: 99 size: 10 skip rate: 0 extended?: True protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: SELECTEDLOOPS:LOOP begin end cut skip_rate extended protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: LOOP start: 96 stop: 105 cut: 99 size: 10 skip rate: 0 extended?: True protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: protocols.loops.loops_main: Pose fold tree FOLD_TREE EDGE 1 95 -1 EDGE 95 99 -1 EDGE 95 106 1 EDGE 106 100 -1 EDGE 106 222 -1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: Setting extended torsions: LOOP start: 96 stop: 105 cut: 99 size: 10 skip rate: 0 extended?: True protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: Building Loop: LOOP start: 96 stop: 105 cut: 99 size: 10 skip rate: 0 extended?: True protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: Building Loop attempt: 0 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: perturb_one_loop_with_KIC: 96 10 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: remodel init temp: 2 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: remodel final temp: 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: kinematic initial perturb with start_res: 96 middle res: 100 end_res: 105 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: loop rmsd before initial kinematic perturbation:0 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: Attempting loop building: 0 ... protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: initial kinematic perturbation complete protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: loop rmsd after initial kinematic perturbation:11.9182 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 170.551 170.551 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 11.0763 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.6364 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.5883 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.5985 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1746 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1911 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.2394 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1761 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.15 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1239 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.121 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1374 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1249 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.13 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.2337 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.0651 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1827 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1362 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.133 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1201 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1851 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.167 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.1628 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.6417 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.5483 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 10.6339 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.92159 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.90439 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.77689 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.26137 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.06095 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.02627 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.02098 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.00016 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.00136 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.00569 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.75676 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.52249 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.51758 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.53895 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.55897 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.56005 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.57554 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.5735 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.54808 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.54239 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.53209 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.91914 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.4496 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.31894 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.3228 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.32357 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.67185 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.5643 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.58706 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.53534 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.54269 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.54524 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.53547 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.29784 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.42985 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.43286 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.17144 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.1681 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.16612 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.16678 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.11865 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.13175 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.12268 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14802 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14837 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14092 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14159 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.16318 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14378 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.13822 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.07149 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.06658 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.15027 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14046 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00037 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.04371 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14842 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.45823 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.49755 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50236 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50233 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.58516 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.55702 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.55727 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.54923 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.53885 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.53407 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.5451 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.56151 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.49471 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50958 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.52329 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50364 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.4458 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.51472 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.51338 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50579 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50984 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50548 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.42239 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.35058 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.4885 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.50467 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.06541 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.06495 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.08361 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.23629 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.14155 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.359 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.34686 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.33365 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.34255 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.11517 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.2088 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.20484 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.26867 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.25896 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.27774 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.27553 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.26616 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.27395 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.27573 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.27277 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.84373 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.84299 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.38439 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.44519 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.41737 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.37791 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.44065 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.51265 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.51067 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.48148 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.4732 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.49185 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.8875 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.88657 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.88324 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 9.00081 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.70792 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.70839 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.70063 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.66137 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.65389 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.64826 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.48551 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.54821 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 8.55236 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.43312 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.34194 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33569 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33668 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33294 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.68564 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.49741 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.45567 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.44466 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.45753 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.4545 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.46116 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.40465 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.42044 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.31304 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.46978 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.56376 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.55135 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.51193 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.46781 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.45875 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.31551 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.31986 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.32701 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.36032 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.30047 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.29107 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.28594 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.31591 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.3725 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.3844 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50515 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.52541 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.48616 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.4874 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.4693 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.48608 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50904 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.49316 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.48859 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50413 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.76197 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.75255 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.32015 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.2443 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.26776 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.49845 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.49877 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.24429 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.17852 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.35643 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.47053 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50111 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.52338 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.51375 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50813 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.49349 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.59626 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.6 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.57097 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.58821 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.57189 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.57974 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.70847 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.7074 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.68739 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.75391 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.81305 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.86492 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.84485 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.83328 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.86881 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.86779 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.15463 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.0909 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.21764 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.19003 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.21663 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.20559 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.19877 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.08961 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.13521 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.15159 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.17848 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.17802 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.11468 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.11327 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.94726 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.95421 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90985 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.85896 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.86876 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87261 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87315 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90442 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90194 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.9175 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92788 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.89771 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90475 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.9312 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91573 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.8907 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92522 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91506 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87576 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87761 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90674 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14757 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.03762 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.03669 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.951 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.89108 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.89309 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.89161 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.88705 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.97811 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.96607 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.96242 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.95567 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.97149 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.97079 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.94814 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.95443 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.95405 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.94305 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93816 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91981 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.88757 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.88761 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00731 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.9952 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.08738 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.09003 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.04589 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.32869 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.24499 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.25475 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.36073 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.35927 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.43856 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.41772 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.3876 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.40461 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.38614 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.40932 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.4221 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.48918 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.56617 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.53331 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.53837 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.75715 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.76681 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.75903 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 5.76658 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.51063 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.5941 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.59348 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.60222 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.73118 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.76056 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.72575 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.7777 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.79709 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.80469 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.79136 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.79603 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.78346 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.84717 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.84718 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.85528 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.97475 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93209 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92944 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93323 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92247 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.9251 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92255 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91205 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92072 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92086 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91505 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91237 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90206 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.9086 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90029 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90025 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93782 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92631 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91236 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92005 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.9227 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92377 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93866 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.94447 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93297 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93943 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.93957 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91254 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87869 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87378 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.84142 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.04452 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.03716 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.03399 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.04258 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.15963 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.1331 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.12541 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.16697 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14867 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.0914 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.09299 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.08873 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.10756 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.96336 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00212 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00619 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.03513 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.04402 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00423 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00184 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.00533 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.92766 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90408 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.81625 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.84407 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.84755 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.8599 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.88223 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.88509 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91242 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.91346 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.90071 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87432 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.87433 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.69258 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.70534 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.61986 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.7389 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.73992 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.15904 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.3123 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.31118 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.27208 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.30053 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.287 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.28713 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33857 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.36858 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.3757 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.36633 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.39483 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.40765 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.39744 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.38999 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.37904 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.3812 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.38515 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.38621 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.35587 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.36439 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.34724 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33745 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33814 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.33817 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.34548 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.34546 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.32397 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.32861 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.32645 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.3436 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.32095 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.30444 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.32292 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.31054 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.24745 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.10007 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.13198 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.12702 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.1369 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.14375 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.20756 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.47283 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.3844 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.39547 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.5625 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.56529 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.55653 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.55116 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.54382 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.59948 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.60444 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.29713 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.04394 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.0397 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.07066 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.81024 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 7.85835 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.61856 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.24378 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.24579 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.24655 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.23749 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.22384 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50007 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.52678 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.53409 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50081 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.50825 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.49945 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.48473 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.47474 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: new centroid perturb rmsd: 6.4629 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: result of loop closure:0 success, 3 failure 0 protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC: Loopstat: 96 105 96 105 10 time 79.0 0 time 0.0 -56.0746 ext protocols.antibody.ModelCDRH3: Finished Modeling Centroid CDR H3 loop protocols.antibody.ModelCDRH3: Finished applying CDR H3 modeler protocols::checkpoint: Deleting checkpoints of LoopMover protocols.antibody.AntibodyModelerProtocol: Full-atom cst_weight: 0 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 protocols.antibody.CDRsMinPackMin: FOLD_TREE EDGE 1 25 -1 EDGE 25 31 -1 EDGE 25 36 1 EDGE 36 32 -1 EDGE 36 49 -1 EDGE 49 58 -1 EDGE 49 66 2 EDGE 66 59 -1 EDGE 66 97 -1 EDGE 97 99 -1 EDGE 97 106 3 EDGE 106 100 -1 EDGE 106 138 -1 EDGE 138 144 -1 EDGE 138 150 4 EDGE 150 145 -1 EDGE 150 164 -1 EDGE 164 168 -1 EDGE 164 172 5 EDGE 172 169 -1 EDGE 172 203 -1 EDGE 203 208 -1 EDGE 203 213 6 EDGE 213 209 -1 EDGE 213 222 -1 protocols.loops.loops_main: Added cutpoint variant to residue 31 protocols.loops.loops_main: Added cutpoint variant to residue 32 protocols.loops.loops_main: Added cutpoint variant to residue 58 protocols.loops.loops_main: Added cutpoint variant to residue 59 protocols.loops.loops_main: Added cutpoint variant to residue 99 protocols.loops.loops_main: Added cutpoint variant to residue 100 protocols.loops.loops_main: Added cutpoint variant to residue 144 protocols.loops.loops_main: Added cutpoint variant to residue 145 protocols.loops.loops_main: Added cutpoint variant to residue 168 protocols.loops.loops_main: Added cutpoint variant to residue 169 protocols.loops.loops_main: Added cutpoint variant to residue 208 protocols.loops.loops_main: Added cutpoint variant to residue 209 core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/chao/rosetta/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.095673 seconds to load from binary core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 11440 rotamers at 141 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 32326220 bytes protocols.antibody.RefineBetaBarrel: start finalize_setup function ... basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score core.pack.task: Packer task: initialize from command line() protocols.antibody.RefineBetaBarrel: FOLD_TREE EDGE 1 25 -1 EDGE 25 31 -1 EDGE 25 36 7 EDGE 36 32 -1 EDGE 36 37 -1 EDGE 37 49 -1 EDGE 49 58 -1 EDGE 49 66 2 EDGE 66 59 -1 EDGE 66 97 -1 EDGE 97 99 -1 EDGE 97 106 3 EDGE 106 100 -1 EDGE 106 115 -1 EDGE 37 137 1 EDGE 137 116 -1 EDGE 137 138 -1 EDGE 138 144 -1 EDGE 138 150 4 EDGE 150 145 -1 EDGE 150 164 -1 EDGE 164 168 -1 EDGE 164 172 5 EDGE 172 169 -1 EDGE 172 203 -1 EDGE 203 208 -1 EDGE 203 213 6 EDGE 213 209 -1 EDGE 213 222 -1 protocols.loops.loops_main: Added cutpoint variant to residue 31 protocols.loops.loops_main: Added cutpoint variant to residue 32 protocols.loops.loops_main: Added cutpoint variant to residue 58 protocols.loops.loops_main: Added cutpoint variant to residue 59 protocols.loops.loops_main: Added cutpoint variant to residue 99 protocols.loops.loops_main: Added cutpoint variant to residue 100 protocols.loops.loops_main: Residue 115 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Residue 116 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Added cutpoint variant to residue 144 protocols.loops.loops_main: Added cutpoint variant to residue 145 protocols.loops.loops_main: Added cutpoint variant to residue 168 protocols.loops.loops_main: Added cutpoint variant to residue 169 protocols.loops.loops_main: Added cutpoint variant to residue 208 protocols.loops.loops_main: Added cutpoint variant to residue 209 protocols.antibody.RefineBetaBarrel: finish finalize_setup function !!! protocols.antibody.LHRepulsiveRamp: start apply function ... protocols.antibody.LHRepulsiveRamp: repulsive ramp cycle 1: rep_weight = 0.02 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: 2 /// protocols.docking.DockMCMCycle: /// Scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.338) (fa_rep 0.02) (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) (chainbreak 1) (overlap_chainbreak 3.33333) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: 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.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 0.9375) (fa_intra_rep 0.005) (fa_elec 0.875) (pro_close 1.25) (hbond_sr_bb 1.17) (hbond_lr_bb 1.17) (hbond_bb_sc 1.17) (hbond_sc 1.1) (dslf_fa13 1.25) (rama 0.25) (omega 0.625) (fa_dun 0.7) (p_aa_pp 0.4) (yhh_planarity 0.625) (ref 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.773742 0.443793 -1.63002 -1.96094 0.61937 0.173326 0.388298 1.0806 -0.358574 0.761128 0.249477 -1.19118 -0.250485 -1.51717 -0.32436 0.165383 0.20134 0.979644 1.23413 0.162496 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 1 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 2 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 3 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 4 protocols.antibody.LHRepulsiveRamp: repulsive ramp cycle 2: rep_weight = 0.10284 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: 2 /// protocols.docking.DockMCMCycle: /// Scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 0.338) (fa_rep 0.10284) (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) (chainbreak 1) (overlap_chainbreak 3.33333) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: 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.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 0.9375) (fa_intra_rep 0.005) (fa_elec 0.875) (pro_close 1.25) (hbond_sr_bb 1.17) (hbond_lr_bb 1.17) (hbond_bb_sc 1.17) (hbond_sc 1.1) (dslf_fa13 1.25) (rama 0.25) (omega 0.625) (fa_dun 0.7) (p_aa_pp 0.4) (yhh_planarity 0.625) (ref 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.773742 0.443793 -1.63002 -1.96094 0.61937 0.173326 0.388298 1.0806 -0.358574 0.761128 0.249477 -1.19118 -0.250485 -1.51717 -0.32436 0.165383 0.20134 0.979644 1.23413 0.162496 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 1 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 2 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 3 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 4 protocols.antibody.LHRepulsiveRamp: repulsive ramp cycle 3: rep_weight = 0.18568 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: 2 /// protocols.docking.DockMCMCycle: /// Scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (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) (chainbreak 1) (overlap_chainbreak 3.33333) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: 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.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 0.9375) (fa_intra_rep 0.005) (fa_elec 0.875) (pro_close 1.25) (hbond_sr_bb 1.17) (hbond_lr_bb 1.17) (hbond_bb_sc 1.17) (hbond_sc 1.1) (dslf_fa13 1.25) (rama 0.25) (omega 0.625) (fa_dun 0.7) (p_aa_pp 0.4) (yhh_planarity 0.625) (ref 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.773742 0.443793 -1.63002 -1.96094 0.61937 0.173326 0.388298 1.0806 -0.358574 0.761128 0.249477 -1.19118 -0.250485 -1.51717 -0.32436 0.165383 0.20134 0.979644 1.23413 0.162496 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 1 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 2 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 3 core.pack.task: Packer task: initialize from command line() protocols.antibody.LHRepulsiveRamp: doing rb_mover_min_trial in the DockMCMCycle ... 4 protocols.antibody.LHRepulsiveRamp: finish apply function !!! protocols.antibody.RefineBetaBarrel: finish repulsive ramping ! 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 0.338) (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) (chainbreak 1) (overlap_chainbreak 3.33333) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: 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.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: /// Packing scorefunction: /// protocols.docking.DockMCMCycle: ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 0.9375) (fa_intra_rep 0.005) (fa_elec 0.875) (pro_close 1.25) (hbond_sr_bb 1.17) (hbond_lr_bb 1.17) (hbond_bb_sc 1.17) (hbond_sc 1.1) (dslf_fa13 1.25) (rama 0.25) (omega 0.625) (fa_dun 0.7) (p_aa_pp 0.4) (yhh_planarity 0.625) (ref 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.773742 0.443793 -1.63002 -1.96094 0.61937 0.173326 0.388298 1.0806 -0.358574 0.761128 0.249477 -1.19118 -0.250485 -1.51717 -0.32436 0.165383 0.20134 0.979644 1.23413 0.162496 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ 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: elec_sigmoidal_die: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D: 78 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_D0: 2 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_sigmoidal_S: 0.36 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_DNA_DNA: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: EnergyMethodOptions::show: envsmooth_zero_negatives: false 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: exclude_intra_res_protein_: true protocols.docking.DockMCMCycle: HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: HBondOptions::show: put_intra_into_total_: 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_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: mphbond: false protocols.docking.DockMCMCycle: HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: protocols.docking.DockMCMCycle: //////////////////////////////////////////////////////////////////////////////// core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2466 rotamers at 40 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 3474836 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2712 rotamers at 42 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 3948828 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2823 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4060972 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2868 rotamers at 42 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4080348 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2640 rotamers at 40 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 3693152 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2788 rotamers at 43 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 3863452 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.antibody.RefineBetaBarrel: finish L_H Docking ! protocols.antibody.RefineBetaBarrel: FINISH BETA BARREL REFINEMENT STEP !! protocols.antibody.RefineOneCDRLoop: Trying Refinement ................. 1 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine init temp: 1.5 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refine final temp: 0.5 core.pack.task: Packer task: initialize from command line() protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: Not designing core.pack.pack_rotamers: built 3697 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9196916 bytes core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -248.448 -248.448 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 1 -330.166 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 1/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 1.96718 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -338.062 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.9729 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -341.424 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 2/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.61322 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.757 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 3/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.61718 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -350.678 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.62088 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -350.046 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 4/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.62367 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -350.083 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 5/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.63969 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.266 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 6/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 7/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 8/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.70934 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.112 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 9/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.77711 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.809 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.77328 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.421 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 10/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 11/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 12/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 13/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.77547 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.505 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 14/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 15/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.76968 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.7 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 16/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.8247 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.841 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 17/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 18/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 19/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 20/80 core.pack.pack_rotamers: built 3610 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 8334720 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -352.057 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -355.841 -355.841 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -355.841 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.8242 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.848 core.pack.pack_rotamers: built 3579 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 8169712 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -355.529 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -355.545 -355.848 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -355.545 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.82346 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.547 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 21/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.94521 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.874 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 22/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 23/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 24/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 25/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 26/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 27/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 28/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 29/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 30/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 31/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.93208 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.655 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 32/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 33/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 34/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 35/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 36/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 37/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 38/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 39/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 40/80 core.pack.pack_rotamers: built 3493 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 7671780 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -355.196 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -357.655 -357.655 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -357.655 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.93202 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.72 core.pack.pack_rotamers: built 3506 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 7852860 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -355.359 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -357.72 -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.93196 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 41/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.94059 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.013 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 42/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.96399 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -356.961 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 43/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 44/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 45/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 46/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.96821 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.113 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 47/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 48/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 49/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 50/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.95717 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.133 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 51/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 52/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 53/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 54/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 55/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.97083 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.729 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 56/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.97306 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.937 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 57/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.98114 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.553 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 58/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.98248 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.753 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.98885 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.199 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 59/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.98698 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.005 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 60/80 core.pack.pack_rotamers: built 3537 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 7936708 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -350.183 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -352.005 -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -352.005 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.98698 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.023 core.pack.pack_rotamers: built 3689 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9325520 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -141.213 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -351.841 -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -351.841 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.73504 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.167 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 61/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 62/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.67026 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.769 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 63/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.67013 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.241 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 64/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.70425 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.275 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 65/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 66/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.56412 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.334 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 67/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 68/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 69/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.53364 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.293 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 70/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 71/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.53949 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -356.792 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 72/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 73/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.54003 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.357 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 74/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.54211 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.398 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 75/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.5332 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -356.097 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 76/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 77/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 78/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 79/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 1/5 80/80 core.pack.pack_rotamers: built 3741 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9688884 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -348.934 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -356.097 -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -356.097 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.53355 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -356.392 core.pack.pack_rotamers: built 3730 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9176204 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -350.01 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -357.415 -357.72 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -357.415 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.53236 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.512 core.pack.pack_rotamers: built 3703 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9061416 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -358.569 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -358.659 -358.659 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -358.659 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 2 -351.605 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 1/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 2/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 3/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.60574 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.735 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.67479 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.97 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 4/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 5/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 6/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 7/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 8/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 9/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 10/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 11/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 12/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.6326 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.851 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 13/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.62995 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.703 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 14/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.63359 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.452 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.6242 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.099 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 15/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.62665 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.144 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 16/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 17/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 18/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 19/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.63124 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.866 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.62915 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.189 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 20/80 core.pack.pack_rotamers: built 3666 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 8797156 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -347.542 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -351.189 -353.851 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -351.189 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.6295 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.207 core.pack.pack_rotamers: built 3754 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9476524 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -350.902 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -350.948 -353.851 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -350.948 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.60246 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -350.967 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 21/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.58443 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -347.343 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.59681 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.039 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 22/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 23/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 24/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 25/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 26/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 27/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.58036 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -350.178 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 28/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.55801 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -349.919 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 29/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 30/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.5572 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -350.163 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.9819 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.676 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 31/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 32/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 33/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 1.98935 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.308 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 34/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 35/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.07781 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.065 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 36/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.05698 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.086 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 37/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 38/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.05797 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.032 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 39/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.22147 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.174 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 40/80 core.pack.pack_rotamers: built 3719 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9595292 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -348.552 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -354.174 -354.174 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -354.174 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.22171 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.408 core.pack.pack_rotamers: built 3680 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 8633516 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -349.864 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -354.878 -354.878 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -354.878 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.16804 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.152 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 41/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.15236 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.799 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 42/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 43/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.15311 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.64 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 44/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 45/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.16257 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.359 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 46/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 47/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 48/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 49/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.16237 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -355.4 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.15357 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.935 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 50/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.11598 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.072 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.10282 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.544 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 51/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 52/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 53/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.1002 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.692 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 54/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 55/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.10252 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.51 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 56/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 57/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.18154 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.492 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 58/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.19282 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.501 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 59/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.19066 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.583 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 60/80 core.pack.pack_rotamers: built 3668 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9135272 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -350.081 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -352.583 -355.799 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -352.583 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.19065 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.603 core.pack.pack_rotamers: built 3670 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 8947324 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -350.771 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -352.603 -355.799 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -352.603 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.19065 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.619 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 61/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 62/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 63/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.1101 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.67 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.06066 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.966 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 64/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.04334 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -353.938 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 65/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 66/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 67/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.04278 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -354.189 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 68/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 69/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.03217 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -352.158 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 70/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.03959 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.181 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 71/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.93781 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.113 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 72/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 73/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 1.84778 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.681 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 74/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 75/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 76/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 1.85031 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.633 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 77/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 1.84337 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -351.266 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 78/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 79/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 2/5 80/80 core.pack.pack_rotamers: built 3834 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9720028 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -345.764 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -356.693 -356.693 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -356.693 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.68446 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.247 core.pack.pack_rotamers: built 3818 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9762712 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -328.391 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -357.247 -357.247 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -357.247 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.68462 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -357.25 core.pack.pack_rotamers: built 3797 rotamers at 46 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 9686656 bytes protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after design: -357.25 protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -357.255 -357.255 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after repack: -357.255 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: cycle: 3 -348.486 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 1/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 2/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 3/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 4/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.65473 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -348.581 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 5/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 6/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.68497 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -346.301 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 7/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.68504 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -346.437 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 8/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 1 move on loop 1: 2.61163 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -347.399 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 9/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: RMS to native after accepted kinematic round 2 move on loop 1: 2.61342 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: energy after accepted move: -348.37 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 10/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 11/80 protocols.loops.loop_mover.refine.LoopMover_Refine_KIC: refinement cycle (outer/inner): 3/5 12/80 protocols.loops.loop_mover