--SREFLEX LOG --VERSION: ATSAS 2.8.4 (r10552) --REFERENCE: Panjkovich & Svergun (2016) PCCP 18, 5707-19 --DATE and TIME: 2019-02-19 18:52:57 --INPUT SAS data type set to X-ray (SAXS) --INPUT SAS data filename: merge_001_FLhuman_final.dat --INPUT PDB filename: SASDC52_fit2_model1.pdb --INPUT PDB contains 4756 ATOM entries, of which 661 are centroids. WARNING - Input structure contains 3 clashes. --Initial Chi2: 14.032 --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: 1:58,59:409,410:598,599:661 --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: 75 conformers. --R --STRUCTURAL FILTERS: FINISHED --R --CONFORMERS: SORTING ACCORDING TO Chi2 --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 75 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: FINISHED --R stage status, level: 1 --R current convergence ratio: 0.000745175 --R (current/previous Chi2) = 7.451/9999) --R List of conformers in current cycle: --R Chi2 modes --R 7.5 n9s3 --R 8.3 n9s2 --R 10.4 n9s1 --R 12.6 n7s-2 --R 12.7 n10s2 --R 12.7 n10s3 --R 13.0 n10s1 --R 13.0 n7s-1 --R 13.1 n13s2 --R 13.1 n10s4 --R 13.2 n13s3 --R 13.3 n7s-3 --R 13.3 n8s1 --R 13.3 n12s1 --R 13.4 n13s1 --R 13.6 n12s2 --R -SCORING: START --R --SCORING: Processing 986 conformers... --R --SCORING JOBS: FINISHED --R --TEMP DIRS: DELETING --R --STRUCTURAL FILTERS PURGING... --R --STRUCTURAL FILTERS INPUT: 986 conformers. --R --STRUCTURAL FILTERS OUTPUT: 612 conformers. --R --STRUCTURAL FILTERS: FINISHED --R --CONFORMERS: SORTING ACCORDING TO Chi2 --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 612 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: FINISHED --R stage status, level: 2 --R current convergence ratio: 0.822172 --R (current/previous Chi2) = 6.126/7.451) --R List of conformers in current cycle: --R Chi2 modes --R 6.1 n9s3xn12s1 --R 6.2 n9s2xn12s2 --R 7.0 n9s3xn15s2 --R 7.0 n9s2xn12s1 --R 7.1 n9s3xn14s1 --R 7.1 n9s3xn14s2 --R 7.4 n9s3xn16s-1 --R 7.6 n7s-1xn9s3 --R 7.7 n9s3xn10s-1 --R 7.7 n9s3xn13s-1 --R 7.7 n9s3xn16s1 --R 7.7 n9s3xn11s-1 --R 7.7 n9s3xn14s3 --R 7.8 n9s3xn13s1 --R 7.8 n8s1xn9s2 --R 7.9 n9s3xn10s-2 --R convergence reached, stage finalizing... --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 15 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 15 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 1 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 1 conformers. --C --STRUCTURAL FILTERS OUTPUT: 1 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 1 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 1 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 12 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 12 conformers. --C --STRUCTURAL FILTERS OUTPUT: 11 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 11 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 11 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 4 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 4 conformers. --C --STRUCTURAL FILTERS OUTPUT: 1 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 1 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 1 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 9 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 9 conformers. --C --STRUCTURAL FILTERS OUTPUT: 9 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 9 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 9 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 18 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 18 conformers. --C --STRUCTURAL FILTERS OUTPUT: 18 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 18 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 3 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 3 conformers. --C --STRUCTURAL FILTERS OUTPUT: 1 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 1 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 1 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 3 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 3 conformers. --C --STRUCTURAL FILTERS OUTPUT: 2 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 2 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 2 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 -SCORING: START --C --SCORING: Processing 11 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 11 conformers. --C --STRUCTURAL FILTERS OUTPUT: 11 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 11 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 11 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: 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 59 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 59 conformers. --C --STRUCTURAL FILTERS OUTPUT: 39 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 39 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 3 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 3 conformers. --C --STRUCTURAL FILTERS OUTPUT: 3 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 3 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 3 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 8 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 8 conformers. --C --STRUCTURAL FILTERS OUTPUT: 6 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 6 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 6 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 26 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 26 conformers. --C --STRUCTURAL FILTERS OUTPUT: 22 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 22 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 16 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 16 conformers. --C --STRUCTURAL FILTERS OUTPUT: 16 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 16 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 15 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 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 9 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 9 conformers. --C --STRUCTURAL FILTERS OUTPUT: 9 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 9 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 9 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 23 conformers... --C --SCORING JOBS: FINISHED --C --TEMP DIRS: DELETING --C --STRUCTURAL FILTERS PURGING... --C --STRUCTURAL FILTERS INPUT: 23 conformers. --C --STRUCTURAL FILTERS OUTPUT: 23 conformers. --C --STRUCTURAL FILTERS: FINISHED --C --CONFORMERS: SORTING ACCORDING TO Chi2 --C --REDUNDANCY: START --C --REDUNDANCY INPUT: 23 conformers. --C --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --C --REDUNDANCY: FINISHED --C -SCORING: FINISHED --C WARNING: CONCOORD failed to generate conformers. --C Check input structure or try again without CONCOORD option --C ++ CONCOORD STAGE: FINISHED --RUNTIME: 284.30 minutes, 8 CPU cores/threads. --SREFLEX: FINISHED 2019-02-19 23:37:15