[Usage about antibody.static.linuxgccrelease] core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

[Tangbbmc]

dell@dell-OptiPlex-Tower-Plus-7010:~/Documents/Software/PW570$ antibody.static.linuxgccrelease -fasta 4m5y_Fv.fasta
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  core.init: Checking for fconfig files in pwd and ./rosetta/flags
  core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
  core.init: command: antibody.static.linuxgccrelease -fasta 4m5y_Fv.fasta
  basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=2102075736 seed_offset=0 real_seed=2102075736
  basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=2102075736 RG_type=mt19937
  core.init: Resolved executable path: /usr/local/rosetta3.14/rosetta/main/source/build/src/release/linux/5.4/64/x86/gcc/7/static/antibody.static.linuxgccrelease
  core.init: Looking for database based on location of executable: /usr/local/rosetta3.14/rosetta/main/database/
  antibody: Using antibody grafting_database at: /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody/
  antibody: Unzipping files in antibody_database (if any). This will only be done once.
  antibody: Done unzipping.
  antibody: Heavy chain fasta input file: 4m5y_Fv.fasta
  antibody: Light chain fasta input file: 4m5y_Fv.fasta
  antibody: Antibody grafting protocol Running with input:
  antibody: SCS_MultiTemplate protocol enabled multi-template regions: orientation
  antibody: Heavy chain sequence: EVQLVESGPGLVKPSDILSLTCAVSGYSISSNYYWGWIRQPPGKGLEWIGSIYHSGSTYYKPSLESRLGISVDTSKNQFSLKLSFVSAADTAVYYCARHVRSGYPDTAYYFDKWGQGTLVTVS
  antibody: Light chain sequence: SYVLTQPPSVSVAPGETARISCGGNNIGTKVLHWYQQTPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEVGDEADYYCQVWDISTDQAVFGGGTKLTVL
  protocols.antibody.grafting: Path to REGEX file is: /usr/local/rosetta3.14/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)GA-Z
  protocols.antibody.grafting: H1 detected: GYSISSNYYWG (11 residues at positions: 25 to 36)
  protocols.antibody.grafting: H3 detected: HVRSGYPDTAYYFDK (15 residues at positions: 98 to 113)
  protocols.antibody.grafting: H2 detected: SIYHSGSTYYKPSLES (16 residues at positions: 50 to 66)
  protocols.antibody.grafting: L1 detected: GGNNIGTKVLH (11 residues at positions: 22 to 33)
  protocols.antibody.grafting: L3 detected: QVWDISTDQAV (11 residues at positions: 87 to 98)
  protocols.antibody.grafting: L2 detected: DDSDRPS (7 residues at positions: 48 to 55)

]}avyAntibodyFramework{fr1[0:25, length=25, EVQLVESGPGLVKPSDILSLTCAVS], fr2[36:50, length=14, WIRQPPGKGLEWIG], fr3[66:98, length=32, RLGISVDTSKNQFSLKLSFVSAADTAVYYCAR], fr4[113:125, length=12, WGQGTLVTVS
]}ghtAntibodyFramework{fr1[0:22, length=22, SYVLTQPPSVSVAPGETARISC], fr2[33:48, length=15, WYQQTPGQAPVLVVY], fr3[55:87, length=32, GIPERFSGSNSGNTATLTISRVEVGDEADYYC], fr4[98:110, length=12, FGGGTKLTVL

protocols.antibody.grafting: Setting antibody grafting database path from command line-options to: /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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
protocols.antibody.grafting.util: Reading file: /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//info/antibody.info
basic.execute: Running blast+ for frh... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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]
protocols.antibody.grafting.util: Reading file: grafting/frh.align
basic.execute: Running blast+ for h1... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//blast_database/database.H1.11, -query, grafting/h1.fasta, -out, grafting/h1.align, -word_size, 2, -outfmt, 7, -max_target_seqs, 1024, -evalue, 2000, -matrix, PAM30]
protocols.antibody.grafting.util: Reading file: grafting/h1.align
basic.execute: Running blast+ for h2... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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]
protocols.antibody.grafting.util: Reading file: grafting/h2.align
basic.execute: Running blast+ for h3... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//blast_database/database.H3.15, -query, grafting/h3.fasta, -out, grafting/h3.align, -word_size, 2, -outfmt, 7, -max_target_seqs, 1024, -evalue, 2000, -matrix, PAM30]
protocols.antibody.grafting.util: Reading file: grafting/h3.align
basic.execute: Running blast+ for frl... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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]
protocols.antibody.grafting.util: Reading file: grafting/frl.align
basic.execute: Running blast+ for l1... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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]
protocols.antibody.grafting.util: Reading file: grafting/l1.align
basic.execute: Running blast+ for l2... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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]
protocols.antibody.grafting.util: Reading file: grafting/l2.align
basic.execute: Running blast+ for l3... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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]
protocols.antibody.grafting.util: Reading file: grafting/l3.align
basic.execute: Running blast+ for orientation... blastp [-db, /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/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.util: Reading file: grafting/orientation.align
protocols.antibody.grafting.util: Reading file: /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody/info/bfactors.info
protocols.antibody.grafting.util: Reading file: /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody/info/orientations.txt
protocols.antibody.grafting.util: Reading file: /usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody/outlier_list
protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 5ukr
protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 5ukp
protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 5uko
protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 5ukn
protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 3ijh
protocols.antibody.grafting: Not enought templates for region h3 was selected... Adding arbitrary template 6cyf
protocols.antibody.grafting: SCS_Base::select: Final results count: h1:91 h2:237 h3:10 l1:34 l2:56 l3:22 frh:954 frl:939 orientation:820
antibody: SCS frh best template: 4m5y
antibody: SCS frl best template: 3mlr
antibody: SCS Orientation best template: 1dn0
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.282191 seconds.
core.import_pose.import_pose: File '/usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//antibody_database/4m5y_trunc.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 123
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO:CtermProteinFull 234
core.conformation.Conformation: Found disulfide between residues 22 96
core.conformation.Conformation: Found disulfide between residues 145 210
core.import_pose.import_pose: File '/usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//antibody_database/3mlr_trunc.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 123
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN:CtermProteinFull 241
core.conformation.Conformation: Found disulfide between residues 22 96
core.conformation.Conformation: Found disulfide between residues 145 210
core.import_pose.import_pose: File '/usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//antibody_database/1dn0_trunc.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 119
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 229
core.conformation.Conformation: Found disulfide between residues 22 95
core.conformation.Conformation: Found disulfide between residues 142 208
protocols.antibody.grafting: Adjusting frh template sequence [/usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//antibody_database/4m5y_trunc.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 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 100D 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113 114
core.conformation.Conformation: Found disulfide between residues 22 96
protocols.antibody.grafting: Sequence before: EVQLVESGPGLVKPSDILSLTCAVSGYSISSNYYWGWIRQPPGKGLEWIGSIYHSGSTYYKPSLESRLGISVDTSKNQFSLKLSFVSAADTAVYYCARHVRSGYPDTAYYFDKWGQGTLVTVS
protocols.simple_moves.MutateResidue: Breaking disulfide bond between CYS96 and CYS22.
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 GLU 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.
protocols.antibody.grafting: [ WARNING ] Was not able to adjust all residue in chain: H!!!
protocols.antibody.grafting: [ WARNING ] Leftovers numbering: [112, 113, 114] AA: S
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, 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, 100D, 100E, 100F, 100G, 101, 102]
protocols.antibody.grafting: [ WARNING ] fr4 : [103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114]
protocols.antibody.grafting: [ WARNING ] }
protocols.antibody.grafting: Sequence after: EVQLVESGPGLVKPSDILSLTCAVSGYSISSNYYWGWIRQPPGKGLEWIGSIYHSGSTYYKPSLESRLGISVDTSKNQFSLKLSFVSAADTAVYYCARHVRSGYPDTAYYFDKWGQGTLVTVS
core.conformation.Conformation: Found disulfide between residues 22 95
protocols.antibody.grafting: Adjusting frl template sequence [/usr/local/rosetta3.14/rosetta/main/database/additional_protocol_data/antibody//antibody_database/3mlr_trunc.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 99 100 101 102 103 104 105 106 107 108 109
core.conformation.Conformation: Found disulfide between residues 22 87
protocols.antibody.grafting: Sequence before: SYDLTQPPSVSVSPGQTASISCSGDKLDDKYVSWYYQRPGQSPVLLMYQDFKRPSGIPERLSGSKSGKTATLTISGTQSLDEGDYYCQAWDASTGVSGGGTKLTVLFGDGTRLTVLGQ
core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

Segmentation fault (core dumped)