core.init: Mini-Rosetta version 53436 from https://svn.rosettacommons.org/source/trunk/rosetta/rosetta_source core.init: command: /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_model_CDR_H3.static.linuxgccrelease -seed_offset 22 -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -s model.pdb -constraints:cst_file ../cter_constraint -scorefile score.sf -multiple_processes_writing_to_one_directory -ex1 -ex2 -antibody::remodel perturb_kic -antibody::snugfit true -antibody::refine refine_kic -antibody::cter_insert false -antibody::flank_residue_min true -antibody::h3_filter true -antibody:constrain_cter -antibody::h3_filter_tolerance 3 -nstruct 100 core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1953151753 seed_offset=22 real_seed=1953151775 core.init.random: RandomGenerator:init: Normal mode, seed=1953151775 RG_type=mt19937 protocols.antibody2.AntibodyModelerProtocol: Setting Up defaults.......... protocols.antibody2.AntibodyModelerProtocol: Start Reading and Setting Options ... protocols.antibody2.AntibodyModelerProtocol: Finish Reading and Setting Options !!! core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 protocols.antibody2: //////////////////////////////////////////////////////////////////////////////// protocols.antibody2: /// protocols.antibody2: /// Rosetta 3 Antibody Modeler /// protocols.antibody2: /// /// protocols.antibody2: /// camelid : 0 protocols.antibody2: /// protocols.antibody2: /// ****** model_h3 : 1 protocols.antibody2: /// h3_perturb_type = 'perturb_kic' protocols.antibody2: /// cter_insert = 0 protocols.antibody2: /// h3_filter = 1 protocols.antibody2: /// protocols.antibody2: /// ****** snugfit : 1 protocols.antibody2: /// LH_repulsive_ramp = 1 protocols.antibody2: /// protocols.antibody2: /// ****** refine_h3 : 1 protocols.antibody2: /// h3_refine_type = 'refine_kic' protocols.antibody2: /// h3_filter = 1 protocols.antibody2: /// h3_filter_tolerance = 3 protocols.antibody2: /// protocols.antibody2: //////////////////////////////////////////////////////////////////////////////// protocols.antibody2: protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 1 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 2 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 3 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 4 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 5 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 6 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 7 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 8 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 9 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 10 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 11 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 12 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 13 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 14 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 15 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 16 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 17 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 18 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 19 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 20 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 21 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 22 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 23 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 24 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 25 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 26 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 27 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 28 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 29 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 30 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 31 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 32 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 33 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 34 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 35 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 36 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 37 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 38 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 39 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 40 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 41 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 42 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 43 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 44 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 45 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 46 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 47 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 48 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 49 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 50 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 51 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 52 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 53 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 54 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 55 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 56 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 57 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 58 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 59 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 60 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 61 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 62 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 63 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 64 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 65 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 66 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 67 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 68 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 69 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 70 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 71 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 72 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 73 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 74 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 75 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 76 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 77 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 78 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 79 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 80 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 81 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 82 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 83 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 84 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 85 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 86 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 87 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 88 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 89 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 90 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 91 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 92 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 93 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 94 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 95 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 96 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 97 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 98 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 99 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 100 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB model.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6242 residue types core.conformation.Conformation: Found disulfide between residues 132 206 core.conformation.Conformation: current variant for 132 CYS core.conformation.Conformation: current variant for 206 CYS core.conformation.Conformation: current variant for 132 CYD core.conformation.Conformation: current variant for 206 CYD core.pack.task: Packer task: initialize from command line() protocols.antibody2.AntibodyModelerProtocol: AAAAAAAA cst_weight: 1 core.io.constraints: read constraints from ../cter_constraint core.io.constraints: Read in 1 constraints protocols.antibody2.AntibodyModelerProtocol: Danger Will Robinson! Native is an impostor! protocols.antibody2.AntibodyModelerProtocol: 'native_pose' is just a copy of the 'input_pose' protocols.antibody2.AntibodyModelerProtocol: since you didn't sepcifiy the native pdb name antibody2.AntibodyInfo: Successfully finished the CDR defintion antibody2.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody2.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody2.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 protocols.antibody2.AntibodyModelerProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody2.AntibodyModelerProtocol: /// Rosetta Antibody Info /// protocols.antibody2.AntibodyModelerProtocol: /// /// protocols.antibody2.AntibodyModelerProtocol: /// Antibody Type: Regular Antibody protocols.antibody2.AntibodyModelerProtocol: /// Predict H3 Cterminus Base: KINKED protocols.antibody2.AntibodyModelerProtocol: /// protocols.antibody2.AntibodyModelerProtocol: /// H1 info: protocols.antibody2.AntibodyModelerProtocol: /// length: 10 protocols.antibody2.AntibodyModelerProtocol: /// sequence: GYTFTNYGMN protocols.antibody2.AntibodyModelerProtocol: /// loop_info: LOOP 136 145 141 0 0 protocols.antibody2.AntibodyModelerProtocol: /// H2 info: protocols.antibody2.AntibodyModelerProtocol: /// length: 17 protocols.antibody2.AntibodyModelerProtocol: /// sequence: WINTYTGEPTYADDFKE protocols.antibody2.AntibodyModelerProtocol: /// loop_info: LOOP 160 176 168 0 0 protocols.antibody2.AntibodyModelerProtocol: /// H3 info: protocols.antibody2.AntibodyModelerProtocol: /// length: 14 protocols.antibody2.AntibodyModelerProtocol: /// sequence: DYYGSTYPYYAMDY protocols.antibody2.AntibodyModelerProtocol: /// loop_info: LOOP 209 222 210 0 0 protocols.antibody2.AntibodyModelerProtocol: /// L1 info: protocols.antibody2.AntibodyModelerProtocol: /// length: 12 protocols.antibody2.AntibodyModelerProtocol: /// sequence: RASSSVSSSYLH protocols.antibody2.AntibodyModelerProtocol: /// loop_info: LOOP 24 35 30 0 0 protocols.antibody2.AntibodyModelerProtocol: /// L2 info: protocols.antibody2.AntibodyModelerProtocol: /// length: 7 protocols.antibody2.AntibodyModelerProtocol: /// sequence: STSNLAS protocols.antibody2.AntibodyModelerProtocol: /// loop_info: LOOP 51 57 54 0 0 protocols.antibody2.AntibodyModelerProtocol: /// L3 info: protocols.antibody2.AntibodyModelerProtocol: /// length: 9 protocols.antibody2.AntibodyModelerProtocol: /// sequence: QQYSGYPYT protocols.antibody2.AntibodyModelerProtocol: /// loop_info: LOOP 90 98 94 0 0 protocols.antibody2.AntibodyModelerProtocol: //////////////////////////////////////////////////////////////////////////////// protocols.antibody2.AntibodyModelerProtocol: protocols.antibody2.H3CterInsert: Reading CDR H3 C-ter Fragments protocols.antibody2.H3CterInsert: LOOP 209 222 210 0 0 protocols.antibody2.H3CterInsert: cdr_h3_size=14 protocols.antibody2.H3CterInsert: aa_1name.size()=18 protocols.antibody2.H3CterInsert: ARDYYGSTYPYYAMDYWG protocols.antibody2.H3CterInsert: Finished reading CDR H3 C-ter Fragments protocols.antibody2.ModelCDRH3: Applying CDR H3 modeler antibody2.AntibodyUtil: Utility: Setting up simple one loop fold tree antibody2.AntibodyUtil: Utility: Finished setting up simple one loop fold tree core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1980 residue types core.import_pose.import_pose: PDB File:./hfr.pdb not found!