--SREFLEX LOG --VERSION: ATSAS 2.8.3 (r9988) --REFERENCE: Panjkovich & Svergun (2016) PCCP 18, 5707-19 --DATE and TIME: 2018-01-03 23:11:03 --INPUT SAS data type set to X-ray (SAXS) --INPUT SAS data filename: Rv1989c_Rv1989cbuf_0236_sub_cut.dat --INPUT PDB filename: FINAL_TA_PDB_ChainB.pdb --INPUT PDB contains 1404 ATOM entries, of which 183 are centroids. --INPUT PDB: HETATM entries present (3 molecules parsed). --Initial Chi2: 4.654 --CPU cores/threads that will be used: 8 --NMA: Running initial normal mode analysis... --DOMDEF: DOMAIN DEFINITION --DOMDEF source: AUTO --DOMDEF: Running automatic structure partition... --DOMDEF: 1:23,24:57,58:91,92:164,165:183 --R ++ RESTRAINED STAGE: START --R RESTRAINED STAGE: generating conformers... --R -SCORING: START --R --SCORING: Processing 100 conformers... --R --SCORING JOBS: FINISHED --R --TEMP DIRS: DELETING --R --STRUCTURAL FILTERS PURGING... --R --STRUCTURAL FILTERS INPUT: 100 conformers. --R --STRUCTURAL FILTERS OUTPUT: 50 conformers. --R --STRUCTURAL FILTERS: FINISHED --R --CONFORMERS: SORTING ACCORDING TO Chi2 --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 50 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: FINISHED --R stage status, level: 1 --R current convergence ratio: 0.000161616 --R (current/previous Chi2) = 1.616/9999) --R List of conformers in current cycle: --R Chi2 modes --R 1.6 n8s-2 --R 1.8 n16s1 --R 2.1 n12s-2 --R 2.2 n10s2 --R 2.2 n9s1 --R 2.4 n11s1 --R 2.5 n8s-1 --R 2.5 n10s3 --R 2.5 n9s2 --R 2.6 n7s1 --R 2.8 n15s-2 --R 2.9 n11s2 --R 2.9 n14s2 --R 2.9 n10s1 --R 3.0 n15s2 --R 3.0 n7s2 --R -SCORING: START --R --SCORING: Processing 856 conformers... --R --SCORING JOBS: FINISHED --R --TEMP DIRS: DELETING --R --STRUCTURAL FILTERS PURGING... --R --STRUCTURAL FILTERS INPUT: 856 conformers. --R --STRUCTURAL FILTERS OUTPUT: 311 conformers. --R --STRUCTURAL FILTERS: FINISHED --R --CONFORMERS: SORTING ACCORDING TO Chi2 --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 311 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: FINISHED --R stage status, level: 2 --R current convergence ratio: 0.801361 --R (current/previous Chi2) = 1.295/1.616) --R List of conformers in current cycle: --R Chi2 modes --R 1.3 n11s1xn16s1 --R 1.5 n8s-2xn9s-1 --R 1.5 n10s1xn16s1 --R 1.5 n8s-2xn12s1 --R 1.5 n7s1xn14s2 --R 1.5 n12s-2xn16s1 --R 1.6 n8s-1xn13s-1 --R 1.6 n8s-2xn10s1 --R 1.6 n9s1xn16s1 --R 1.6 n8s-2 --R 1.6 n8s-1xn10s2 --R 1.6 n8s-1xn15s-2 --R 1.6 n7s1xn16s1 --R 1.7 n11s1xn14s2 --R 1.7 n8s-1xn11s1 --R 1.7 n8s-2xn11s-1 --R convergence reached, stage finalizing... --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 32 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: START --R --SCORING: Processing 5 conformers... --R --SCORING JOBS: FINISHED --R --TEMP DIRS: DELETING --R --STRUCTURAL FILTERS PURGING... --R --STRUCTURAL FILTERS INPUT: 5 conformers. --R --STRUCTURAL FILTERS OUTPUT: 5 conformers. --R --STRUCTURAL FILTERS: FINISHED --R --CONFORMERS: SORTING ACCORDING TO Chi2 --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 5 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 5 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: FINISHED --R OUTPUT: fit file written to output_sreflex/fits/rc01.fit --R OUTPUT: fit file written to output_sreflex/fits/rc02.fit --R OUTPUT: fit file written to output_sreflex/fits/rc03.fit --R OUTPUT: fit file written to output_sreflex/fits/rc04.fit --R OUTPUT: fit file written to output_sreflex/fits/rc05.fit --R OUTPUT: model coordinates written to output_sreflex/models/rc01.pdb --R OUTPUT: model coordinates written to output_sreflex/models/rc02.pdb --R OUTPUT: model coordinates written to output_sreflex/models/rc03.pdb --R OUTPUT: model coordinates written to output_sreflex/models/rc04.pdb --R OUTPUT: model coordinates written to output_sreflex/models/rc05.pdb --R ++ RESTRAINED STAGE: FINISHED ++ CONCOORD STAGE: START --C CONCOORD STAGE: generating conformers... --C About to run CONCOORD on conformer nr. 1 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 2 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 3 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 11 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 4 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 13 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 5 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 6 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 7 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 15 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 8 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C About to run CONCOORD on conformer nr. 9 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 10 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 15 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 11 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 12 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 13 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 14 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 14 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 15 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 12 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 16 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C About to run CONCOORD on conformer nr. 17 cycle: 1 --C Removing non-standard protein/nucleotide atoms for CONCOORD --C Executing CONCOORD... --C CONCOORD call finished --C -SCORING: START --C --SCORING: Processing 100 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 100 conformers. --C --STRUCTURAL FILTERS OUTPUT: 100 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 100 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 9 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C -SCORING: START --C --SCORING: Processing 5 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 5 conformers. --C --STRUCTURAL FILTERS OUTPUT: 5 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 5 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 5 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C OUTPUT: fit file written to output_sreflex/fits/cc01.fit --C OUTPUT: fit file written to output_sreflex/fits/cc02.fit --C OUTPUT: fit file written to output_sreflex/fits/cc03.fit --C OUTPUT: fit file written to output_sreflex/fits/cc04.fit --C OUTPUT: fit file written to output_sreflex/fits/cc05.fit --C OUTPUT: model coordinates written to output_sreflex/models/cc01.pdb --C OUTPUT: model coordinates written to output_sreflex/models/cc02.pdb --C OUTPUT: model coordinates written to output_sreflex/models/cc03.pdb --C OUTPUT: model coordinates written to output_sreflex/models/cc04.pdb --C OUTPUT: model coordinates written to output_sreflex/models/cc05.pdb --C ++ CONCOORD STAGE: FINISHED --RUNTIME: 12.82 minutes, 8 CPU cores/threads. --SREFLEX: FINISHED 2018-01-03 23:23:52