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", 
  "profit": "profit", 
  "rosetta_bin": "/home/rosie/rosie/rosie.back/data/antibody/bin", 
  "rosetta_database": "/home/rosie/rosie/rosie.back/data/antibody/rosetta_database", 
  "rosetta_platform": "static.linuxgccrelease", 
  "scripts": "/home/rosie/rosie/rosie.back/data/antibody/scripts", 
  "working_dir": "/home/rosie/rosie/rosie.back/Jobs/Job_01378/"
}
Antibody job input json: {
  "model_h3_loop": 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 --profit profit --prefix=output/  --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
Could not find output/details/... creating it...
Rosetta Antibody script [Python, version 2.0]. Starting...
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_databse: /home/rosie/rosie/rosie.back/data/antibody/rosetta_database

Light chain: 'ENVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC'
Heavy chain: 'AVQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGG'
CDR: {
  "FRH": "AVQLEQELKKPGETVKISCKASWVKQKWMGRFAFSLETSASAAYLQINNLKNEDTATYFCARWGQGTTVTVSSA", 
  "FRL": "ENVLTQIMSASPGEKVTMTCWYQQKLWIYGVPARFSGSGYSLTISSVEAEDAATYYCFGGGTKLEIKRA", 
  "FR_H1": "AVQLEQSGPELKKPGETVKISCKAS", 
  "FR_H2": "WVKQAPGKGLKWMG", 
  "FR_H3": "RFAFSLETSASAAYLQINNLKNEDTATYFCAR", 
  "FR_H4": "WGQGTTVTVSSA", 
  "FR_L1": "ENVLTQSPAIMSASPGEKVTMTC", 
  "FR_L2": "WYQQKSGASPKLWIY", 
  "FR_L3": "GVPARFSGSGSGTSYSLTISSVEAEDAATYYC", 
  "FR_L4": "FGGGTKLEIKRA", 
  "H1": "GYTFTNYGMN", 
  "H2": "WINTYTGEPTYADDFKE", 
  "H3": "DYYGSTYPYYAMDY", 
  "L1": "RASSSVSSSYLH", 
  "L2": "STSNLAS", 
  "L3": "QQYSGYPYT", 
  "heavy": "AVQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQG", 
  "light": "ENVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGG", 
  "light_heavy": "ENVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGGAVQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQG"
}

Running blast as: /home/rosie/prefix/blast+/bin/blastp
With datbase in:/home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database
The template for FRL is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1eo8_chothia.pdb
The template for FRH is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb2adf_chothia.pdb
The template for light is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1v7m_chothia.pdb
The template for heavy is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb3ojd_chothia.pdb
The template for L1 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1ors_chothia.pdb
The template for L2 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb3oz9_chothia.pdb
The template for L3 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb2b2x_chothia.pdb
The template for H1 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb4d9q_chothia.pdb
The template for H2 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1a4j_chothia.pdb
The template for H3 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb2qhr_chothia.pdb
The template for light_heavy is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1uwx_chothia.pdb

Running antibody_assemble as: /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_assemble_CDRs.static.linuxgccrelease
With rosetta_datbase in:/home/rosie/rosie/rosie.back/data/antibody/rosetta_database

Running idealize as: /home/rosie/rosie/rosie.back/data/antibody/bin/idealize_jd2.static.linuxgccrelease
With rosetta_datbase in:/home/rosie/rosie/rosie.back/data/antibody/rosetta_database

Running idealize as: /home/rosie/rosie/rosie.back/data/antibody/bin/relax.static.linuxgccrelease
With rosetta_datbase in:/home/rosie/rosie/rosie.back/data/antibody/rosetta_database

Preparing the cter_constraint file of the subsequent H3 modeling for the query...
H3: 14 DYYGSTYPYYAMDY 	Keys residues:  LEU LEU TYR ALA ARG ALA MET ASP
Predicted base conformation is KINK
Done!
Moving starting files to output/details dir...
cp output/* output/details/
cp: omitting directory `output/details'
cp: omitting directory `output/logs'

Encounter error while executing:  cp output/* output/details/