Antibody submit script, running with args: { "antibody_root": "/home/rosie/rosie/rosie.back/data/antibody", "blast": "/home/rosie/prefix/blast+/bin/blastp", "daemon_id": "GrayLab.Jazz", "data": "/home/rosie/rosie/rosie.back/data", "debug": false, "here": "/home/rosie/rosie/rosie.back", "hpc_driver": "Condor", "log_dir": "/home/rosie/rosie/rosie.back/Jobs/22185/output/logs", "profit": "profit", "remote": "false", "rosetta_bin": "/home/rosie/rosie/rosie.back/data/antibody/bin", "rosetta_database": "/home/rosie/rosie/rosie.back/data/antibody/rosetta_database", "rosetta_mpi_platform": "static.linuxgccrelease", "rosetta_platform": "static.linuxgccrelease", "scripts": "/home/rosie/rosie/rosie.back/data/antibody/scripts", "working_dir": "/home/rosie/rosie/rosie.back/Jobs/22185" } Antibody job input json: { "model_h3_loop": true, "multiple_template_grafting": true } Running Antibody script... /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody.py --light-chain input/light_chain.fasta --heavy-chain input/heavy_chain.fasta --blast /home/rosie/prefix/blast+/bin/blastp --blast-database /home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database --antibody-database /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database --superimpose-profit profit --prefix=output/ --skip-kink-constraints --rosetta-bin /home/rosie/rosie/rosie.back/data/antibody/bin --rosetta-platform static.linuxgccrelease --rosetta-database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database --multi-template-grafting --number-of-templates 10 --light_heavy-multi-graft --filter-by-orientational-distance=1 --orientational-distance-cutoff 0.5 Rosetta Antibody script [Python, version 2.0]. Starting... Could not find output/details/... creating it... Output prefix: output/ Blast database: /home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database Antibody database: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database rosetta_bin: /home/rosie/rosie/rosie.back/data/antibody/bin [platform: static.linuxgccrelease] rosetta_database: /home/rosie/rosie/rosie.back/data/antibody/rosetta_database Using full antibody database (no homolog exclusion) Idealize: False Relax: True Light chain: ENVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC Heavy chain: AVQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGG L1 detected: RASSSVSSSYLH (12 residues at positions 23 to 34) L3 detected: QQYSGYPYT ( 9 residues at positions 89 to 97) L2 detected: STSNLAS (7 residues at positions 50 to 56) FR_L1: ENVLTQSPAIMSASPGEKVTMTC FR_L2: WYQQKSGASPKLWIY FR_L3: GVPARFSGSGSGTSYSLTISSVEAEDAATYYC FR_L4: FGGGTKLEIKRA L segments: ENVLTQSPAIMSASPGEKVTMTC RASSSVSSSYLH WYQQKSGASPKLWIY STSNLAS GVPARFSGSGSGTSYSLTISSVEAEDAATYYC QQYSGYPYT FGGGTKLEIKRA H1 detected: GYTFTNYGMN (10 residues at positions 25 to 34) H3 detected: DYYGSTYPYYAMDY (14 residues at positions 98 to 111) H2 detected: WINTYTGEPTYADDFKE (17 residues at positions 49 to 65) FR_H1: AVQLEQSGPELKKPGETVKISCKAS FR_H2: WVKQAPGKGLKWMG FR_H3: RFAFSLETSASAAYLQINNLKNEDTATYFCAR FR_H4: WGQGTTVTVSSA H segments: AVQLEQSGPELKKPGETVKISCKAS GYTFTNYGMN WVKQAPGKGLKWMG WINTYTGEPTYADDFKE RFAFSLETSASAAYLQINNLKNEDTATYFCAR DYYGSTYPYYAMDY WGQGTTVTVSSA Running /home/rosie/prefix/blast+/bin/blastp I: Queryname=FRL I: Found 600 blast results (limit 600) Could not find output/details/filters/... creating it... FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb FRL template: pdb1mim_chothia.pdb I: Queryname=FRH I: Found 600 blast results (limit 600) FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb FRH template: pdb2adf_chothia.pdb I: Queryname=light I: Found 600 blast results (limit 600) light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb light template: pdb3oz9_chothia.pdb I: Queryname=heavy I: Found 600 blast results (limit 600) heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb heavy template: pdb3ojd_chothia.pdb I: Queryname=L1 I: Found 33 blast results (limit 600) L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb L1 template: pdb1ors_chothia.pdb I: Queryname=L2 I: Found 104 blast results (limit 600) L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb L2 template: pdb3oz9_chothia.pdb I: Queryname=L3 I: Found 245 blast results (limit 600) L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb L3 template: pdb2b2x_chothia.pdb I: Queryname=H1 I: Found 423 blast results (limit 600) H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb H1 template: pdb4d9q_chothia.pdb I: Queryname=H2 I: Found 158 blast results (limit 600) H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb H2 template: pdb1a4j_chothia.pdb I: Queryname=H3 I: Found 17 blast results (limit 600) H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb H3 template: pdb2qhr_chothia.pdb I: Queryname=light_heavy I: Found 605 blast results (limit 600) light_heavy template: pdb1uwx_chothia.pdb light_heavy template: pdb1i7z_chothia.pdb light_heavy template: pdb1ncc_chothia.pdb light_heavy template: pdb1nca_chothia.pdb light_heavy template: pdb1ncb_chothia.pdb light_heavy template: pdb1a4k_chothia.pdb light_heavy template: pdb2adf_chothia.pdb light_heavy template: pdb1nlb_chothia.pdb light_heavy template: pdb1c1e_chothia.pdb light_heavy template: pdb1mhh_chothia.pdb Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Rosetta run terminated with Error 65280 ! The command executed was: cd 'output/details' && /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -overwrite -s FR0.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false Error: Could not run essential antibody_graft application. Cannot continue. Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Rosetta run terminated with Error 65280 ! The command executed was: cd 'output/details' && /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -overwrite -s FR1.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false Error: Could not run essential antibody_graft application. Cannot continue. Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Running relax as /home/rosie/rosie/rosie.back/data/antibody/bin/relax.static.linuxgccrelease Preparing cter_constraint file for H3 modeling H3: 14 DYYGSTYPYYAMDY Key residues: TYR LEU TYR ALA ARG ALA MET ASP Predicted base conformation is KINK Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Running relax as /home/rosie/rosie/rosie.back/data/antibody/bin/relax.static.linuxgccrelease Preparing cter_constraint file for H3 modeling H3: 14 DYYGSTYPYYAMDY Key residues: TYR LEU TYR ALA ARG ALA MET ASP Predicted base conformation is KINK Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Rosetta run terminated with Error 65280 ! The command executed was: cd 'output/details' && /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -overwrite -s FR4.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false Error: Could not run essential antibody_graft application. Cannot continue. Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Running relax as /home/rosie/rosie/rosie.back/data/antibody/bin/relax.static.linuxgccrelease Preparing cter_constraint file for H3 modeling H3: 14 DYYGSTYPYYAMDY Key residues: TYR LEU TYR ALA ARG ALA MET ASP Predicted base conformation is KINK Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Rosetta run terminated with Error 65280 ! The command executed was: cd 'output/details' && /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -overwrite -s FR6.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false Error: Could not run essential antibody_graft application. Cannot continue. Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Running relax as /home/rosie/rosie/rosie.back/data/antibody/bin/relax.static.linuxgccrelease Preparing cter_constraint file for H3 modeling H3: 14 DYYGSTYPYYAMDY Key residues: TYR LEU TYR ALA ARG ALA MET ASP Predicted base conformation is KINK Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Running relax as /home/rosie/rosie/rosie.back/data/antibody/bin/relax.static.linuxgccrelease Preparing cter_constraint file for H3 modeling H3: 14 DYYGSTYPYYAMDY Key residues: TYR LEU TYR ALA ARG ALA MET ASP Predicted base conformation is KINK Running ProFit... Running antibody_graft Running antibody_graft as /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease Rosetta run terminated with Error 65280 ! The command executed was: cd 'output/details' && /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_graft.static.linuxgccrelease -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -overwrite -s FR9.pdb -antibody::h3_no_stem_graft -scorefile score-graft.sf -check_cdr_chainbreaks false Error: Could not run essential antibody_graft application. Cannot continue. Run time 2188.93 s Done!