core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534 core.init: command: antibody_designer.linuxgccrelease -s 5ugyOut.pdb -primary_cdrs H3 -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -light_chain lambda -random_start -nstruct 1 core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-2055576823 seed_offset=0 real_seed=-2055576823 core.init.random: RandomGenerator:init: Normal mode, seed=-2055576823 RG_type=mt19937 core.init: Resolved executable path: /home/tongf/rosetta_bin_linux_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/antibody_designer.default.linuxgccrelease core.init: Looking for database based on location of executable: /home/tongf/rosetta_bin_linux_2018.33.60351_bundle/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 5ugyOut.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 5ugyOut.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.89 seconds. core.import_pose.import_pose: File '5ugyOut.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: Loading 'NAG' from the PDB components dictionary for residue type 'pdb_NAG' core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 403 A BMA BMAA core.io.pose_from_sfr.PoseFromSFRBuilder: missing: N core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 403 C BMA BMAA core.io.pose_from_sfr.PoseFromSFRBuilder: missing: N core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 403 E BMA BMAA core.io.pose_from_sfr.PoseFromSFRBuilder: missing: N core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.io.pose_from_sfr.PoseFromSFRBuilder: missing: C core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 323, 326 A core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 1038, 326 C core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 1543, 326 E core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 653 in file 5ugyOut.pdb. Best match rsd_type: HIS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1158 in file 5ugyOut.pdb. Best match rsd_type: HIS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1663 in file 5ugyOut.pdb. Best match rsd_type: HIS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1726 in file 5ugyOut.pdb. Best match rsd_type: GLU:NtermProteinFull core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1947 in file 5ugyOut.pdb. Best match rsd_type: GLU:NtermProteinFull core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 2168 in file 5ugyOut.pdb. Best match rsd_type: GLU:NtermProteinFull core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 323 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 324 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 325 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 326 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 327 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 328 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 329 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 330 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 331 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 541 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 714 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 1037 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1038 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1039 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1040 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1041 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1042 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1043 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1044 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1045 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 1218 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 1541 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1542 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1543 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1544 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1545 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1546 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1547 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1548 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 1549 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 1722 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 1943 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 2164 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 2385 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 2595 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 2805 core.conformation.Conformation: Found disulfide between residues 5 678 core.conformation.Conformation: current variant for 5 CYS core.conformation.Conformation: current variant for 678 CYS core.conformation.Conformation: current variant for 5 CYD core.conformation.Conformation: current variant for 678 CYD core.conformation.Conformation: Found disulfide between residues 43 275 core.conformation.Conformation: current variant for 43 CYS core.conformation.Conformation: current variant for 275 CYS core.conformation.Conformation: current variant for 43 CYD core.conformation.Conformation: current variant for 275 CYD core.conformation.Conformation: Found disulfide between residues 56 68 core.conformation.Conformation: current variant for 56 CYS core.conformation.Conformation: current variant for 68 CYS core.conformation.Conformation: current variant for 56 CYD core.conformation.Conformation: current variant for 68 CYD core.conformation.Conformation: Found disulfide between residues 91 136 core.conformation.Conformation: current variant for 91 CYS core.conformation.Conformation: current variant for 136 CYS core.conformation.Conformation: current variant for 91 CYD core.conformation.Conformation: current variant for 136 CYD core.conformation.Conformation: Found disulfide between residues 279 303 core.conformation.Conformation: current variant for 279 CYS core.conformation.Conformation: current variant for 303 CYS core.conformation.Conformation: current variant for 279 CYD core.conformation.Conformation: current variant for 303 CYD core.conformation.Conformation: Found disulfide between residues 352 417 core.conformation.Conformation: current variant for 352 CYS core.conformation.Conformation: current variant for 417 CYS core.conformation.Conformation: current variant for 352 CYD core.conformation.Conformation: current variant for 417 CYD core.conformation.Conformation: Found disulfide between residues 466 525 core.conformation.Conformation: current variant for 466 CYS core.conformation.Conformation: current variant for 525 CYS core.conformation.Conformation: current variant for 466 CYD core.conformation.Conformation: current variant for 525 CYD core.conformation.Conformation: Found disulfide between residues 685 689 core.conformation.Conformation: current variant for 685 CYS core.conformation.Conformation: current variant for 689 CYS core.conformation.Conformation: current variant for 685 CYD core.conformation.Conformation: current variant for 689 CYD core.conformation.Conformation: Found disulfide between residues 719 1182 core.conformation.Conformation: current variant for 719 CYS core.conformation.Conformation: current variant for 1182 CYS core.conformation.Conformation: current variant for 719 CYD core.conformation.Conformation: current variant for 1182 CYD core.conformation.Conformation: Found disulfide between residues 757 989 core.conformation.Conformation: current variant for 757 CYS core.conformation.Conformation: current variant for 989 CYS core.conformation.Conformation: current variant for 757 CYD core.conformation.Conformation: current variant for 989 CYD core.conformation.Conformation: Found disulfide between residues 770 782 core.conformation.Conformation: current variant for 770 CYS core.conformation.Conformation: current variant for 782 CYS core.conformation.Conformation: current variant for 770 CYD core.conformation.Conformation: current variant for 782 CYD core.conformation.Conformation: Found disulfide between residues 805 850 core.conformation.Conformation: current variant for 805 CYS core.conformation.Conformation: current variant for 850 CYS core.conformation.Conformation: current variant for 805 CYD core.conformation.Conformation: current variant for 850 CYD core.conformation.Conformation: Found disulfide between residues 993 1017 core.conformation.Conformation: current variant for 993 CYS core.conformation.Conformation: current variant for 1017 CYS core.conformation.Conformation: current variant for 993 CYD core.conformation.Conformation: current variant for 1017 CYD core.conformation.Conformation: Found disulfide between residues 1189 1193 core.conformation.Conformation: current variant for 1189 CYS core.conformation.Conformation: current variant for 1193 CYS core.conformation.Conformation: current variant for 1189 CYD core.conformation.Conformation: current variant for 1193 CYD core.conformation.Conformation: Found disulfide between residues 1223 1686 core.conformation.Conformation: current variant for 1223 CYS core.conformation.Conformation: current variant for 1686 CYS core.conformation.Conformation: current variant for 1223 CYD core.conformation.Conformation: current variant for 1686 CYD core.conformation.Conformation: Found disulfide between residues 1261 1493 core.conformation.Conformation: current variant for 1261 CYS core.conformation.Conformation: current variant for 1493 CYS core.conformation.Conformation: current variant for 1261 CYD core.conformation.Conformation: current variant for 1493 CYD core.conformation.Conformation: Found disulfide between residues 1274 1286 core.conformation.Conformation: current variant for 1274 CYS core.conformation.Conformation: current variant for 1286 CYS core.conformation.Conformation: current variant for 1274 CYD core.conformation.Conformation: current variant for 1286 CYD core.conformation.Conformation: Found disulfide between residues 1309 1354 core.conformation.Conformation: current variant for 1309 CYS core.conformation.Conformation: current variant for 1354 CYS core.conformation.Conformation: current variant for 1309 CYD core.conformation.Conformation: current variant for 1354 CYD core.conformation.Conformation: Found disulfide between residues 1497 1521 core.conformation.Conformation: current variant for 1497 CYS core.conformation.Conformation: current variant for 1521 CYS core.conformation.Conformation: current variant for 1497 CYD core.conformation.Conformation: current variant for 1521 CYD core.conformation.Conformation: Found disulfide between residues 1693 1697 core.conformation.Conformation: current variant for 1693 CYS core.conformation.Conformation: current variant for 1697 CYS core.conformation.Conformation: current variant for 1693 CYD core.conformation.Conformation: current variant for 1697 CYD core.conformation.Conformation: Found disulfide between residues 1744 1818 core.conformation.Conformation: current variant for 1744 CYS core.conformation.Conformation: current variant for 1818 CYS core.conformation.Conformation: current variant for 1744 CYD core.conformation.Conformation: current variant for 1818 CYD core.conformation.Conformation: Found disulfide between residues 1869 1925 core.conformation.Conformation: current variant for 1869 CYS core.conformation.Conformation: current variant for 1925 CYS core.conformation.Conformation: current variant for 1869 CYD core.conformation.Conformation: current variant for 1925 CYD core.conformation.Conformation: Found disulfide between residues 1965 2039 core.conformation.Conformation: current variant for 1965 CYS core.conformation.Conformation: current variant for 2039 CYS core.conformation.Conformation: current variant for 1965 CYD core.conformation.Conformation: current variant for 2039 CYD core.conformation.Conformation: Found disulfide between residues 2090 2146 core.conformation.Conformation: current variant for 2090 CYS core.conformation.Conformation: current variant for 2146 CYS core.conformation.Conformation: current variant for 2090 CYD core.conformation.Conformation: current variant for 2146 CYD core.conformation.Conformation: Found disulfide between residues 2186 2260 core.conformation.Conformation: current variant for 2186 CYS core.conformation.Conformation: current variant for 2260 CYS core.conformation.Conformation: current variant for 2186 CYD core.conformation.Conformation: current variant for 2260 CYD core.conformation.Conformation: Found disulfide between residues 2311 2367 core.conformation.Conformation: current variant for 2311 CYS core.conformation.Conformation: current variant for 2367 CYS core.conformation.Conformation: current variant for 2311 CYD core.conformation.Conformation: current variant for 2367 CYD core.conformation.Conformation: Found disulfide between residues 2406 2471 core.conformation.Conformation: current variant for 2406 CYS core.conformation.Conformation: current variant for 2471 CYS core.conformation.Conformation: current variant for 2406 CYD core.conformation.Conformation: current variant for 2471 CYD core.conformation.Conformation: Found disulfide between residues 2520 2579 core.conformation.Conformation: current variant for 2520 CYS core.conformation.Conformation: current variant for 2579 CYS core.conformation.Conformation: current variant for 2520 CYD core.conformation.Conformation: current variant for 2579 CYD core.conformation.Conformation: Found disulfide between residues 2616 2681 core.conformation.Conformation: current variant for 2616 CYS core.conformation.Conformation: current variant for 2681 CYS core.conformation.Conformation: current variant for 2616 CYD core.conformation.Conformation: current variant for 2681 CYD core.conformation.Conformation: Found disulfide between residues 2730 2789 core.conformation.Conformation: current variant for 2730 CYS core.conformation.Conformation: current variant for 2789 CYS core.conformation.Conformation: current variant for 2730 CYD core.conformation.Conformation: current variant for 2789 CYD core.pack.pack_missing_sidechains: packing residue number 324 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 325 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 326 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 327 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 328 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 329 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 330 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 331 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1038 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1039 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1040 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1041 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1042 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1043 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1044 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1045 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1542 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1543 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1544 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1545 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1546 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1547 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1548 because of missing atom number 10 atom name O1 core.pack.pack_missing_sidechains: packing residue number 1549 because of missing atom number 10 atom name O1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 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/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.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 core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/tongf/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/tongf/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.17 seconds to load from binary core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG core.pack.pack_rotamers: built 159 rotamers at 24 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 21964 bytes 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: ARGGLEPRSVDYYYYGMDVW 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 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 19 Omega: TTTTTTTTTTTTTTTTTTT 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: 11 Omega: TTTTTTTTTTT //////////////////////////////////////////////////////////////////////////////// /// Rosetta Antibody Info /// /// /// /// Antibody Type: Regular Antibody /// Light Chain Type: lambda /// Predict H3 Cterminus Base: KINKED /// /// H1 info: /// length: 13 /// sequence: KASGYTFTDYHIN /// north_cluster: H1-13-1 /// loop_info: LOOP start: 1745 stop: 1757 cut: 1751 size: 13 skip rate: 0 extended?: False /// H2 info: /// length: 10 /// sequence: WIHPNSGDTN /// north_cluster: H2-10-1 /// loop_info: LOOP start: 1772 stop: 1781 cut: 1777 size: 10 skip rate: 0 extended?: False /// H3 info: /// length: 19 /// sequence: ARGGLEPRSVDYYYYGMDV /// north_cluster: H3-19-1 /// loop_info: LOOP start: 1819 stop: 1837 cut: 1820 size: 19 skip rate: 0 extended?: False /// L1 info: /// length: 11 /// sequence: GGNDIGRKSVH /// north_cluster: L1-11-3 /// loop_info: LOOP start: 353 stop: 363 cut: 358 size: 11 skip rate: 0 extended?: False /// L2 info: /// length: 8 /// sequence: CYDSDRPS /// north_cluster: L2-8-1 /// loop_info: LOOP start: 378 stop: 385 cut: 382 size: 8 skip rate: 0 extended?: False /// L3 info: /// length: 11 /// sequence: QVWDSSSDHVI /// north_cluster: L3-11-1 /// loop_info: LOOP start: 418 stop: 428 cut: 423 size: 11 skip rate: 0 extended?: False //////////////////////////////////////////////////////////////////////////////// core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.antibody.design.AntibodyDesignProtocol: Score without constraints: protocols.antibody.design.AntibodyDesignProtocol: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -15482.481 -15482.481 fa_rep 0.550 41366.827 22751.755 fa_sol 1.000 9824.699 9824.699 fa_intra_rep 0.005 5711.927 28.560 fa_intra_sol_xover4 1.000 572.541 572.541 lk_ball_wtd 1.000 -273.963 -273.963 fa_elec 1.000 -2773.784 -2773.784 pro_close 1.250 935.042 1168.803 hbond_sr_bb 1.000 -398.284 -398.284 hbond_lr_bb 1.000 -843.428 -843.428 hbond_bb_sc 1.000 -207.071 -207.071 hbond_sc 1.000 -147.043 -147.043 dslf_fa13 1.250 -28.751 -35.939 atom_pair_constraint 0.010 0.000 0.000 omega 0.400 1531.258 612.503 fa_dun 0.700 6453.012 4517.109 p_aa_pp 0.600 -655.424 -393.254 yhh_planarity 0.625 0.002 0.001 ref 1.000 781.873 781.873 rama_prepro 0.450 1582.032 711.914 --------------------------------------------------- Total weighted score: 20414.514 protocols.antibody.design.AntibodyDesignProtocol: protocols.antibody.design.AntibodyDesignProtocol: /// Run Antibody Designer: true protocols.antibody.design.AntibodyDesignProtocol: // ->Post SnugDock: false protocols.antibody.design.AntibodyDesignProtocol: // ->Post DS Relax: false protocols.antibody.design.AntibodyDesignProtocol: protocols.antibody.design.AntibodyDesignProtocol: Running Graft Design Protocol //////////////////////////////////////////////////////////////////////////////// /// Rosetta Antibody Info /// /// /// /// Antibody Type: Regular Antibody /// Light Chain Type: lambda /// Predict H3 Cterminus Base: KINKED /// /// H1 info: /// length: 13 /// sequence: KASGYTFTDYHIN /// north_cluster: H1-13-1 /// loop_info: LOOP start: 1745 stop: 1757 cut: 1751 size: 13 skip rate: 0 extended?: False /// H2 info: /// length: 10 /// sequence: WIHPNSGDTN /// north_cluster: H2-10-1 /// loop_info: LOOP start: 1772 stop: 1781 cut: 1777 size: 10 skip rate: 0 extended?: False /// H3 info: /// length: 19 /// sequence: ARGGLEPRSVDYYYYGMDV /// north_cluster: H3-19-1 /// loop_info: LOOP start: 1819 stop: 1837 cut: 1820 size: 19 skip rate: 0 extended?: False /// L1 info: /// length: 11 /// sequence: GGNDIGRKSVH /// north_cluster: L1-11-3 /// loop_info: LOOP start: 353 stop: 363 cut: 358 size: 11 skip rate: 0 extended?: False /// L2 info: /// length: 8 /// sequence: CYDSDRPS /// north_cluster: L2-8-1 /// loop_info: LOOP start: 378 stop: 385 cut: 382 size: 8 skip rate: 0 extended?: False /// L3 info: /// length: 11 /// sequence: QVWDSSSDHVI /// north_cluster: L3-11-1 /// loop_info: LOOP start: 418 stop: 428 cut: 423 size: 11 skip rate: 0 extended?: False //////////////////////////////////////////////////////////////////////////////// core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40 basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors. antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 19 Omega: TTTTTTTTTTTTTTTTTTT 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: 11 Omega: TTTTTTTTTTT protocols.antibody.clusters.CDRClusterSet: Adding cacheable cluster data to pose protocols.antibody.NativeAntibodySeq: Setting full pose sequence protocols.antibody.design.util: Reading CDRSetOptions from: /sampling/antibodies/design/default_instructions.txt protocols.antibody.design.util: Reading CDRGraftDesignOptions from: /sampling/antibodies/design/default_instructions.txt protocols.antibody.design.util: Reading CDRSeqDesignOptions from: /sampling/antibodies/design/default_instructions.txt protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job 5ugyOut_0001 File: src/core/pose/chains_util.cc:465 chain_id A represents more than one chain! protocols.jd2.JobDistributor: [ ERROR ] protocols.jd2.JobDistributor: [ WARNING ] 5ugyOut_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 20 seconds Error: [ ERROR ] ERROR: Exception caught by antibody_design application: File: src/protocols/jd2/JobDistributor.cc:329 1 jobs failed; check output for error messages Error: [ ERROR ]