--SREFLEX LOG --VERSION: ATSAS 3.2.1 (r14885) --REFERENCE: Panjkovich & Svergun (2016) PCCP 18, 5707-19 --DATE and TIME: 2023-07-09 08:28:03 --INPUT SAS data type set to X-ray (SAXS) --INPUT SAS data filename: GSN.dat --INPUT PDB filename: gsnca.pdb --INPUT PDB contains 5589 ATOM entries, of which 717 are centroids. --Initial Chi2: 2.90924 --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: 1:125,126:370,371:717 --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: 8.29803e-05 --R (current/previous Chi2) = 0.82972/9999) --R List of conformers in current cycle: --R Chi2 modes --R 0.8 n12s-3 --R 0.9 n12s-4 --R 1.0 n12s-2 --R 1.3 n12s-5 --R 1.7 n12s-1 --R 2.2 n14s2 --R 2.3 n14s1 --R 2.4 n10s-5 --R 2.4 n7s2 --R 2.5 n16s2 --R 2.5 n10s-2 --R 2.5 n10s-4 --R 2.6 n10s-3 --R 2.6 n7s1 --R 2.6 n10s-1 --R 2.7 n11s-1 --R -SCORING: START --R --SCORING: Processing 786 conformers... --R --SCORING JOBS: FINISHED --R --TEMP DIRS: DELETING --R --STRUCTURAL FILTERS PURGING... --R --STRUCTURAL FILTERS INPUT: 786 conformers. --R --STRUCTURAL FILTERS OUTPUT: 446 conformers. --R --STRUCTURAL FILTERS: FINISHED --R --CONFORMERS: SORTING ACCORDING TO Chi2 --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 446 conformers. --R --REDUNDANCY OUTPUT (TOP ONLY): 16 conformers. --R --REDUNDANCY: FINISHED --R -SCORING: FINISHED --R stage status, level: 2 --R current convergence ratio: 0.893694 --R (current/previous Chi2) = 0.741516/0.82972) --R List of conformers in current cycle: --R Chi2 modes --R 0.7 n10s-5xn14s3 --R 0.7 n12s-3xn15s2 --R 0.8 n7s2xn12s-3 --R 0.8 n12s-3xn15s1 --R 0.8 n12s-3xn14s1 --R 0.8 n12s-4xn13s1 --R 0.8 n10s-4xn14s3 --R 0.8 n12s-3xn16s-1 --R 0.8 n12s-4xn15s3 --R 0.8 n7s1xn12s-3 --R 0.8 n12s-5xn13s2 --R 0.8 n12s-4xn15s2 --R 0.8 n12s-4xn13s2 --R 0.8 n11s-1xn12s-3 --R 0.8 n12s-3 --R 0.8 n12s-5xn13s3 --R convergence reached, stage finalizing... --R --REDUNDANCY: START --R --REDUNDANCY INPUT: 17 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_sreflex001/fits/rc01.fit --R OUTPUT: fit file written to output_sreflex001/fits/rc02.fit --R OUTPUT: fit file written to output_sreflex001/fits/rc03.fit --R OUTPUT: fit file written to output_sreflex001/fits/rc04.fit --R OUTPUT: fit file written to output_sreflex001/fits/rc05.fit --R OUTPUT: model coordinates written to output_sreflex001/models/rc01.pdb --R OUTPUT: model coordinates written to output_sreflex001/models/rc02.pdb --R OUTPUT: model coordinates written to output_sreflex001/models/rc03.pdb --R OUTPUT: model coordinates written to output_sreflex001/models/rc04.pdb --R OUTPUT: model coordinates written to output_sreflex001/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 WARNING: CONCOORD failed to generate conformers. --C Check input structure or try again without CONCOORD option --C ++ CONCOORD STAGE: FINISHED --RUNTIME: 126.35 minutes, 8 CPU cores/threads. --SREFLEX: FINISHED 2023-07-09 10:34:24