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:
<ROSETTASCRIPTS>

	<SCOREFXNS>
		<talaris_full weights=talaris2014>
			<Reweight scoretype="coordinate_constraint" weight=0.4/>
			<Reweight scoretype="res_type_constraint" weight=0.4/>
		</talaris_full>

		<soft_rep_full weights=soft_rep>
			<Reweight scoretype="coordinate_constraint" weight=0.4/>
			<Reweight scoretype="res_type_constraint" weight=0.4/>
		</soft_rep_full>

		<tal_no_pssm weights=talaris2014>
			<Reweight scoretype="coordinate_constraint" weight=0.4/>
		</tal_no_pssm>

	 	<talaris_pure weights=talaris2014/>

	</SCOREFXNS>

	<TASKOPERATIONS>
        	<InitializeFromCommandline name=init/>
		<RestrictToRepacking name=rtr/>
 		<PreventResiduesFromRepacking name=fix_res reference_pdb_id="input_example.pdb" residues="1A,2A,3A,4A"/> #any improtant residues
	</TASKOPERATIONS>

	<MOVERS>
        	<PackRotamersMover name=soft_repack scorefxn=soft_rep_full task_operations=init,rtr,fix_res/>
        	<PackRotamersMover name=hard_repack scorefxn=talaris_full task_operations=init,rtr,fix_res/>
        	<RotamerTrialsMinMover name=RTmin scorefxn=talaris_full task_operations=init,rtr,fix_res/>
        	<MinMover name=soft_min scorefxn=soft_rep_full chi=1 bb=1 jump=0/>
        	<MinMover name=hard_min scorefxn=talaris_full chi=1 bb=1 jump=0/>
        	<ConstraintSetMover name=add_CA_cst cst_file="example.cst"/>

        	<ParsedProtocol name = refinement_block> #10 movers
			<Add mover_name=soft_repack/>
			<Add mover_name=soft_min/>
			<Add mover_name=soft_repack/>
			<Add mover_name=hard_min/>
			<Add mover_name=hard_repack/>
			<Add mover_name=hard_min/>
              		<Add mover_name=hard_repack/>
                	<Add mover_name=RTmin/>
                	<Add mover_name=RTmin/>
                	<Add mover_name=hard_min/>
		</ParsedProtocol>

		<LoopOver name = iter4 mover_name = refinement_block iterations = 4/> #16 reacpk+min iterations total
	</MOVERS>

	<FILTERS>
        	<ScoreType name="stability_score_full" scorefxn=talaris_full score_type=total_score confidence=0 threshold=0/>
        	<ScoreType name="stability_without_pssm" scorefxn=tal_no_pssm score_type = total_score confidence=0 threshold=0/>
	       	<ScoreType name="stability_pure" scorefxn=talaris_pure score_type=total_score confidence=0 threshold=0/>
		<Rmsd name="rmsd" confidence = 0/>
		<Time name=timer/>
	</FILTERS>

	<PROTOCOLS>
	#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.
        	<Add filter_name=timer/>
		<Add mover_name=add_CA_cst/>
        	<Add mover_name=iter4/>
        	<Add filter_name=stability_score_full/>
        	<Add filter_name=stability_without_pssm/>
        	<Add filter_name=stability_pure/>
        	<Add filter_name=rmsd/>
		<Add filter_name=timer/>
	</PROTOCOLS>

</ROSETTASCRIPTS>
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 <output filename> to output the schema to a file to see all valid options.
Your XML has failed validation.  The error message below will tell you where in your XML file the error occurred.  Here's how to fix it:

1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file.
2) If you haven’t run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first.  The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction="talaris2014") is a good indicator that this is your problem.
3) If you are a developer and neither 1 nor 2 worked - email the developer’s mailing list or try Slack.
4) If you are an academic or commercial user - try the Rosetta Forums https://www.rosettacommons.org/forum


Error messages were:
Error: AttValue: " or ' expected

1: <ROSETTASCRIPTS>
2: 
3: 	<SCOREFXNS>
4: 		<talaris_full weights=talaris2014>
5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
7: 		</talaris_full>
8: 
9: 		<soft_rep_full weights=soft_rep>
Error: attributes construct error

1: <ROSETTASCRIPTS>
2: 
3: 	<SCOREFXNS>
4: 		<talaris_full weights=talaris2014>
5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
7: 		</talaris_full>
8: 
9: 		<soft_rep_full weights=soft_rep>
Error: Couldn't find end of Start Tag talaris_full line 4

1: <ROSETTASCRIPTS>
2: 
3: 	<SCOREFXNS>
4: 		<talaris_full weights=talaris2014>
5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
7: 		</talaris_full>
8: 
9: 		<soft_rep_full weights=soft_rep>
Error: AttValue: " or ' expected

 1: <ROSETTASCRIPTS>
 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
Error: attributes construct error

 1: <ROSETTASCRIPTS>
 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
Error: Couldn't find end of Start Tag Reweight line 5

 1: <ROSETTASCRIPTS>
 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
Error: AttValue: " or ' expected

 1: <ROSETTASCRIPTS>
 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
Error: attributes construct error

 1: <ROSETTASCRIPTS>
 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
Error: Couldn't find end of Start Tag Reweight line 6

 1: <ROSETTASCRIPTS>
 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
Error: Opening and ending tag mismatch: SCOREFXNS line 3 and talaris_full

 2: 
 3: 	<SCOREFXNS>
 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
Error: AttValue: " or ' expected

 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
Error: attributes construct error

 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
Error: Couldn't find end of Start Tag soft_rep_full line 9

 4: 		<talaris_full weights=talaris2014>
 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
Error: AttValue: " or ' expected

 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
Error: attributes construct error

 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
Error: Couldn't find end of Start Tag Reweight line 10

 5: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
Error: AttValue: " or ' expected

 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
16: 		</tal_no_pssm>
Error: attributes construct error

 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
16: 		</tal_no_pssm>
Error: Couldn't find end of Start Tag Reweight line 11

 6: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
16: 		</tal_no_pssm>
Error: Opening and ending tag mismatch: ROSETTASCRIPTS line 1 and soft_rep_full

 7: 		</talaris_full>
 8: 
 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
16: 		</tal_no_pssm>
17: 
Error: Extra content at the end of the document

 9: 		<soft_rep_full weights=soft_rep>
10: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
11: 			<Reweight scoretype="res_type_constraint" weight=0.4/>
12: 		</soft_rep_full>
13: 
14: 		<tal_no_pssm weights=talaris2014>
15: 			<Reweight scoretype="coordinate_constraint" weight=0.4/>
16: 		</tal_no_pssm>
17: 
18: 	 	<talaris_pure weights=talaris2014/>
19: 
------------------------------------------------------------
Warning messages were:
------------------------------------------------------------

Error: [ ERROR ] 
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: input_example_0001
protocols.jd2.JobDistributor: no more batches to process... 
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 7 seconds
Error: [ ERROR ] Exception caught by rosetta_scripts application:

File: src/protocols/jd2/JobDistributor.cc:328
1 jobs failed; check output for error messages
Error: [ ERROR ]