core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-210 r210 2019.06+release.4d8c807 4d8c8074e4eab340e5d26c0069d807aa5a8d6978 https://www.rosettacommons.org 2019-02-08T22:29:28.907993 core.init: command: antibody.default.linuxgccrelease -fasta mxp335.fasta -antibody::grafting_database /home/mxp/apps/rosetta/tools/antibody core.init: 'RNG device' seed mode, using '/dev/urandom', seed=210016788 seed_offset=0 real_seed=210016788 core.init.random: RandomGenerator:init: Normal mode, seed=210016788 RG_type=mt19937 core.init: Resolved executable path: /home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/antibody.default.linuxgccrelease core.init: Looking for database based on location of executable: /home/mxp/apps/rosetta/main/database/ antibody: Using antibody grafting_database at: /home/mxp/apps/rosetta/tools/antibody antibody: Unzipping files in antibody_database (if any). This will only be done once. antibody: Done unzipping. antibody: Heavy chain fasta input file: mxp335.fasta antibody: Light chain fasta input file: mxp335.fasta antibody: Antibody grafting protocol Running with input: antibody: SCS_MultiTemplate protocol enabled multi-template regions: orientation antibody: Heavy chain sequence: QVQLQESGPGLVKPSDTLSLTCAVSGYSISRSSNWWGWIRQPPGKGLEWIGYIYYSGSTYYNPSLKSRVTMSVDTSKNQFSLKLSSVTAVDTGVYYCARGAMFGDYPMDRWGKGTTVTVSS antibody: Light chain sequence: SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCSSYTSSSTLWVFGTGTKVTVL protocols.antibody.grafting: Path to REGEX file is: /home/mxp/apps/rosetta/main/database/protocol_data/antibody/cdr_regex.txt protocols.antibody.grafting: The detected H1 REGEX is: C[A-Z]{1,16}(W)(I|V|F|Y|A|M|L|N|G)(R|K|Q|V|N|C|G)(Q|K|H|E|L|R) protocols.antibody.grafting: The detected H3 REGEX is: C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R) protocols.antibody.grafting: The detected L1 REGEX is: C[A-Z]{1,17}(WYL|WLQ|WFQ|WYQ|WYH|WVQ|WVR|WWQ|WVK|WYR|WLL|WFL|WVF|WIQ|WYR|WNQ|WHL|WHQ|WYM|WYY) protocols.antibody.grafting: The detected L3 REGEX is: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y) protocols.antibody.grafting: H1 detected: GYSISRSSNWWG (12 residues at positions: 25 to 37) protocols.antibody.grafting: H3 detected: GAMFGDYPMDR (11 residues at positions: 99 to 110) protocols.antibody.grafting: H2 detected: YIYYSGSTYYNPSLKS (16 residues at positions: 51 to 67) protocols.antibody.grafting: L1 detected: GGNNIGSKSVH (11 residues at positions: 22 to 33) protocols.antibody.grafting: L3 detected: SSYTSSSTLWV (11 residues at positions: 87 to 98) protocols.antibody.grafting: L2 detected: DDSDRPS (7 residues at positions: 48 to 55) HeavyAntibodyFramework{fr1[0:25, length=25, QVQLQESGPGLVKPSDTLSLTCAVS], fr2[37:51, length=14, WIRQPPGKGLEWIG], fr3[67:99, length=32, RVTMSVDTSKNQFSLKLSSVTAVDTGVYYCAR], fr4[110:121, length=11, WGKGTTVTVSS]} LightAntibodyFramework{fr1[0:22, length=22, SYVLTQPPSVSVAPGQTARITC], fr2[33:48, length=15, WYQQKPGQAPVLVVY], fr3[55:87, length=32, GIPERFSGSNSGNTATLTISRVEAGDEADYYC], fr4[98:108, length=10, FGTGTKVTVL]} protocols.antibody.grafting: Setting antibody grafting database path from command line-options to: /home/mxp/apps/rosetta/tools/antibody protocols.antibody.grafting: Setting output prefix from command line-options to: grafting/ protocols.antibody.grafting: Setting path to NCBI-Blast+ executable from command line-options to: blastp basic.execute: Running blast+ for frh... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.FRH -query grafting/frh.fasta -out grafting/frh.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62 basic.execute: Running blast+ for h1... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.H1.12 -query grafting/h1.fasta -out grafting/h1.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30 basic.execute: Running blast+ for h2... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.H2.16 -query grafting/h2.fasta -out grafting/h2.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30 basic.execute: Running blast+ for h3... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.H3.11 -query grafting/h3.fasta -out grafting/h3.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30 basic.execute: Running blast+ for frl... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.FRL -query grafting/frl.fasta -out grafting/frl.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62 basic.execute: Running blast+ for l1... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.L1.11 -query grafting/l1.fasta -out grafting/l1.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30 basic.execute: Running blast+ for l2... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.L2.7 -query grafting/l2.fasta -out grafting/l2.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30 basic.execute: Running blast+ for l3... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.L3.11 -query grafting/l3.fasta -out grafting/l3.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30 basic.execute: Running blast+ for orientation... blastp -db /home/mxp/apps/rosetta/tools/antibody/blast_database/database.light_heavy -query grafting/orientation.fasta -out grafting/orientation.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62 protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1acy protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1ai1 protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1etz protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1ggb protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1ggc protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1ggi protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1hys protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1j5o protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1jrh protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1mco protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 12e8 protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1a6u protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1a6v protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1a6w protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1acy protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1ad9 protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1ae6 protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1afv protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 1ai1 protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 12e8 protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 1a14 protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 1a2y protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 1a7n protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 1a7o protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 1a7p protocols.antibody.grafting: Not enought templates for region l1 was selected... Adding arbitrary template 1a7q protocols.antibody.grafting: Not enought templates for region l3 was selected... Adding arbitrary template 1adq protocols.antibody.grafting: Not enought templates for region l3 was selected... Adding arbitrary template 1g9m protocols.antibody.grafting: Not enought templates for region l3 was selected... Adding arbitrary template 1g9n protocols.antibody.grafting: Not enought templates for region l3 was selected... Adding arbitrary template 1gc1 protocols.antibody.grafting: Not enought templates for region l3 was selected... Adding arbitrary template 1nfd antibody: SCS frh best template: 4npy antibody: SCS frl best template: 2dd8 antibody: SCS Orientation best template: 4npy core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 696 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.69 seconds. core.import_pose.import_pose: File '/home/mxp/apps/rosetta/tools/antibody/antibody_database/pdb4npy_chothia.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 130 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 241 core.conformation.Conformation: Found disulfide between residues 21 94 core.conformation.Conformation: current variant for 21 CYS core.conformation.Conformation: current variant for 94 CYS core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 94 CYD core.conformation.Conformation: Found disulfide between residues 152 217 core.conformation.Conformation: current variant for 152 CYS core.conformation.Conformation: current variant for 217 CYS core.conformation.Conformation: current variant for 152 CYD core.conformation.Conformation: current variant for 217 CYD core.import_pose.import_pose: File '/home/mxp/apps/rosetta/tools/antibody/antibody_database/pdb2dd8_chothia.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 109 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 225 core.conformation.Conformation: Found disulfide between residues 22 87 core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 87 CYS core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 87 CYD core.conformation.Conformation: Found disulfide between residues 130 204 core.conformation.Conformation: current variant for 130 CYS core.conformation.Conformation: current variant for 204 CYS core.conformation.Conformation: current variant for 130 CYD core.conformation.Conformation: current variant for 204 CYD core.import_pose.import_pose: File '/home/mxp/apps/rosetta/tools/antibody/antibody_database/pdb4npy_chothia.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 130 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 241 core.conformation.Conformation: Found disulfide between residues 21 94 core.conformation.Conformation: current variant for 21 CYS core.conformation.Conformation: current variant for 94 CYS core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 94 CYD core.conformation.Conformation: Found disulfide between residues 152 217 core.conformation.Conformation: current variant for 152 CYS core.conformation.Conformation: current variant for 217 CYS core.conformation.Conformation: current variant for 152 CYD core.conformation.Conformation: current variant for 217 CYD protocols.antibody.grafting: Adjusting frh template sequence [/home/mxp/apps/rosetta/tools/antibody/antibody_database/pdb4npy_chothia.pdb]... protocols.antibody.grafting: By using numbering: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 31A 31B 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112 113 core.conformation.Conformation: Found disulfide between residues 21 94 core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 94 CYD core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 94 CYD protocols.antibody.grafting: Sequence before: VQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTLHGRRIYGIVAFKEWFTYYYMDVWGKGTTVTVS core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1 core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date! core.conformation.Residue: [ WARNING ] Connection atom name (in src): C core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue VAL 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1 core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date! core.conformation.Residue: [ WARNING ] Connection atom name (in src): C protocols.antibody.grafting: [ WARNING ] Was not able to adjust all residue in chain: H!!! protocols.antibody.grafting: [ WARNING ] Leftovers numbering: [1, 31A, 31B, 112, 113] AA: QSSSS protocols.antibody.grafting: [ WARNING ] Original numbering was: AntibodyChainNumbering { protocols.antibody.grafting: [ WARNING ] fr1 : [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] protocols.antibody.grafting: [ WARNING ] cdr1 : [26, 27, 28, 29, 30, 31, 31A, 31B, 32, 33, 34, 35] protocols.antibody.grafting: [ WARNING ] fr2 : [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] protocols.antibody.grafting: [ WARNING ] cdr2 : [50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65] protocols.antibody.grafting: [ WARNING ] fr3 : [66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 82A, 82B, 82C, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94] protocols.antibody.grafting: [ WARNING ] cdr3 : [95, 96, 97, 98, 99, 100, 100A, 100B, 100C, 101, 102] protocols.antibody.grafting: [ WARNING ] fr4 : [103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113] protocols.antibody.grafting: [ WARNING ] } protocols.antibody.grafting: Sequence after: VQLQESGPGLVKPSDTLSLTCAVSGYSISRNWWGWIRQPPGKGLEWIGYIYYSGSTYYNPSLKSRVTMSVDTSKNQFSLKLSSVTAVDTGVYYCARGAMFGDYPMIVAFKEWFTYYYMDRWGKGTTVTVS core.conformation.Conformation: Found disulfide between residues 21 94 core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 94 CYD core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 94 CYD protocols.antibody.grafting: Adjusting frl template sequence [/home/mxp/apps/rosetta/tools/antibody/antibody_database/pdb2dd8_chothia.pdb]... protocols.antibody.grafting: By using numbering: 1 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 96 97 98 99 100 101 102 103 104 105 106 107 core.conformation.Conformation: Found disulfide between residues 22 87 core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 87 CYD core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 87 CYD protocols.antibody.grafting: Sequence before: SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDYVFGTGTKVTVLGQ core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1 core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date! core.conformation.Residue: [ WARNING ] Connection atom name (in src): C core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue SER 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1 core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date! core.conformation.Residue: [ WARNING ] Connection atom name (in src): C protocols.antibody.grafting: [ WARNING ] Was not able to adjust all residue in chain: L!!! protocols.antibody.grafting: [ WARNING ] Leftovers numbering: [95B] AA: L protocols.antibody.grafting: [ WARNING ] Original numbering was: AntibodyChainNumbering { protocols.antibody.grafting: [ WARNING ] fr1 : [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] protocols.antibody.grafting: [ WARNING ] cdr1 : [24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] protocols.antibody.grafting: [ WARNING ] fr2 : [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] protocols.antibody.grafting: [ WARNING ] cdr2 : [50, 51, 52, 53, 54, 55, 56] protocols.antibody.grafting: [ WARNING ] fr3 : [57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88] protocols.antibody.grafting: [ WARNING ] cdr3 : [89, 90, 91, 92, 93, 94, 95, 95A, 95B, 96, 97] protocols.antibody.grafting: [ WARNING ] fr4 : [98, 99, 100, 101, 102, 103, 104, 105, 106, 107] protocols.antibody.grafting: [ WARNING ] } protocols.antibody.grafting: Sequence after: SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCSSYTSSSTWVFGTGTKVTVLGQ core.conformation.Conformation: Found disulfide between residues 22 87 core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 87 CYD core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 87 CYD protocols.antibody.grafting: Attaching CDR loop: h1, from pdb: 1acy core.import_pose.import_pose: File '/home/mxp/apps/rosetta/tools/antibody/antibody_database/pdb1acy_chothia.pdb' automatically determined to be of type PDB core.io.pdb.HeaderInformation: [ ERROR ] Malformed Compound record found: ' IGG1 FAB FRAGMENT (59.1) COMPLEXED WITH HIV-1 GP120 (MN ISOLATE) FRAGMENT (RESIDUES 308 - 332)' core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 233 core.conformation.Conformation: Found disulfide between residues 23 92 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 92 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 92 CYD core.conformation.Conformation: Found disulfide between residues 135 210 core.conformation.Conformation: current variant for 135 CYS core.conformation.Conformation: current variant for 210 CYS core.conformation.Conformation: current variant for 135 CYD core.conformation.Conformation: current variant for 210 CYD core.conformation.Conformation: Found disulfide between residues 148 167 core.conformation.Conformation: current variant for 148 CYS core.conformation.Conformation: current variant for 167 CYS core.conformation.Conformation: current variant for 148 CYD core.conformation.Conformation: current variant for 167 CYD protocols.antibody.grafting: Grafting... protocols.grafting.CCDEndsGraftMover: Start: 24 End: 35 NterO: 2 CterO: 2 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 10 residues from 25 to 34 core.conformation.Conformation: Found disulfide between residues 21 84 core.conformation.Conformation: current variant for 21 CYS core.conformation.Conformation: current variant for 84 CYS core.conformation.Conformation: current variant for 21 CYD core.conformation.Conformation: current variant for 84 CYD core.conformation.Conformation: Found disulfide between residues 142 207 core.conformation.Conformation: current variant for 142 CYS core.conformation.Conformation: current variant for 207 CYS core.conformation.Conformation: current variant for 142 CYD core.conformation.Conformation: current variant for 207 CYD core.conformation.util: [ ERROR ] Residue 10 was disulfide bonded but had no partner caught exception File: src/core/conformation/util.cc:2375 [ ERROR ] UtilityExitException ERROR: =============================================================== ERROR:: Exit from: src/core/conformation/util.cc line: 2375 BACKTRACE: /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libutility.so(utility::exit(char const*, int, std::string const&, int)+0x277) [0x7f177d84c2a7] /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libprotocols.7.so(utility::exit(char const*, int, int)+0x25) [0x7f178d2df195] /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libcore.2.so(core::conformation::disulfide_bonds(core::conformation::Conformation const&, utility::vector1, std::allocator > >&)+0x581) [0x7f177ed600f1] /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libprotocols_a.5.so(protocols::grafting::insert_pose_into_pose(core::pose::Pose const&, core::pose::Pose const&, unsigned long, unsigned long, bool)+0xaa) [0x7f17872764da] /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libprotocols_a.5.so(protocols::grafting::GraftMoverBase::insert_piece(core::pose::Pose const&, core::pose::Pose&)+0xb8) [0x7f178726f588] /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libprotocols_a.5.so(protocols::grafting::CCDEndsGraftMover::apply(core::pose::Pose&)+0x1b5) [0x7f178726a875] /share/home/mxp/apps/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/8/default/libprotocols.7.so(protocols::antibody::grafting::graft_cdr_loops(protocols::antibody::grafting::AntibodySequence const&, protocols::antibody::grafting::SCS_ResultSet const&, std::string const&, std::string const&, std::string const&, bool, bool)+0x4d3c) [0x7f178d050a0c] antibody.default.linuxgccrelease() [0x41661a] antibody.default.linuxgccrelease() [0x412b84] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f177b5cc3d5] antibody.default.linuxgccrelease() [0x412e14]