core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.source.release-223 r223 2019.22+release.d8f9b4a d8f9b4a90a8f2caa32948bacdb6e551591facd5f https://www.rosettacommons.org 2019-05-31T12:23:20.477246
core.init: command: /home/negi/MANAGER/rosetta_src_2019.22.60749_bundle/main/source//bin/rosetta_scripts.linuxgccrelease -database /home/negi/MANAGER/rosetta_src_2019.22.60749_bundle/main/database -in:file:s input_example.pdb -parser:protocol refine.xml -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=input_example.pdb -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 @flags -overwrite
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1006512244 seed_offset=0 real_seed=-1006512244
core.init.random: RandomGenerator:init: Normal mode, seed=-1006512244 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input_example.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input_example.pdb
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch LowerDNA as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch UpperDNA as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch VirtualDNAPhosphate as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch ShoveBB as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch VirtualBB as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch N_acetylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch C_methylamidated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch SpecialRotamer as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch Cterm_amidation as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch pro_hydroxylated_case1 as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch pro_hydroxylated_case2 as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch ser_phosphorylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch thr_phosphorylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_phosphorylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_sulfated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_monomethylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_dimethylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_trimethylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_acetylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch glu_carboxylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch cys_acetylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_diiodinated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch MethylatedProteinCterm as requested
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 979 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.21344 seconds.
core.import_pose.import_pose: File 'input_example.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=refine.xml
protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%cst_full_path%%'='example.cst'; '%%cst_value%%'='0.4'; '%%pdb_reference%%'='input_example.pdb'; '%%res_to_fix%%'='1A,2A,3A,4A';
protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:
#any improtant residues
#10 movers
#16 reacpk+min iterations total
#1st round is soft design and min, 2nd round is soft design hard min, 3rd and 4th round are hard design and min. In the 4th round also include RT min.
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'input_example_0001'
Error: [ ERROR ]
File: src/protocols/rosetta_scripts/RosettaScriptsParser.cc:1305
Input rosetta scripts XML file "refine.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema