== using base filename at1g16640 == using existing residue numbering == moving into orig_files dir == extracting amino acid sequence from at1g16640.seq == renumbering PDB file at1g16640.pdb, preparing for conversion == moving to /u/volkman/at1g16640/9valid/7e/conversion == running generateProtons.csh copying model 1 to 1xxx_1.pdb copying model 2 to 1xxx_2.pdb copying model 3 to 1xxx_3.pdb copying model 4 to 1xxx_4.pdb copying model 5 to 1xxx_5.pdb copying model 6 to 1xxx_6.pdb copying model 7 to 1xxx_7.pdb copying model 8 to 1xxx_8.pdb copying model 9 to 1xxx_9.pdb copying model 10 to 1xxx_10.pdb copying model 11 to 1xxx_11.pdb copying model 12 to 1xxx_12.pdb copying model 13 to 1xxx_13.pdb copying model 14 to 1xxx_14.pdb copying model 15 to 1xxx_15.pdb copying model 16 to 1xxx_16.pdb copying model 17 to 1xxx_17.pdb copying model 18 to 1xxx_18.pdb copying model 19 to 1xxx_19.pdb copying model 20 to 1xxx_20.pdb Found number of models: 20 doing 1xxx_10.pdb doing 1xxx_11.pdb doing 1xxx_12.pdb doing 1xxx_13.pdb doing 1xxx_14.pdb doing 1xxx_15.pdb doing 1xxx_16.pdb doing 1xxx_17.pdb doing 1xxx_18.pdb doing 1xxx_19.pdb doing 1xxx_1.pdb doing 1xxx_20.pdb doing 1xxx_2.pdb doing 1xxx_3.pdb doing 1xxx_4.pdb doing 1xxx_5.pdb doing 1xxx_6.pdb doing 1xxx_7.pdb doing 1xxx_8.pdb doing 1xxx_9.pdb Found number of models: 20 Found models: 1xxx_10_cns.pdb 1xxx_11_cns.pdb 1xxx_12_cns.pdb 1xxx_13_cns.pdb 1xxx_14_cns.pdb 1xxx_15_cns.pdb 1xxx_16_cns.pdb 1xxx_17_cns.pdb 1xxx_18_cns.pdb 1xxx_19_cns.pdb 1xxx_1_cns.pdb 1xxx_20_cns.pdb 1xxx_2_cns.pdb 1xxx_3_cns.pdb 1xxx_4_cns.pdb 1xxx_5_cns.pdb 1xxx_6_cns.pdb 1xxx_7_cns.pdb 1xxx_8_cns.pdb 1xxx_9_cns.pdb doing model 1 doing model 2 doing model 3 doing model 4 doing model 5 doing model 6 doing model 7 doing model 8 doing model 9 doing model 10 doing model 11 doing model 12 doing model 13 doing model 14 doing model 15 doing model 16 doing model 17 doing model 18 doing model 19 doing model 20 == moving PDB and PSF files to /u/volkman/at1g16640/9valid/7e/input == moving to /u/volkman/at1g16640/9valid/7e/orig_files == converting dihedral constraint file at1g16640.aco to xplor format == converting NOE constraints to xplor format (using aqua) * AQUA scripts directory: /u02/jurgen/src/aqua3.2/scripts * Restraint input file is 1xxx.upl * Restraint output file names begin with 1xxx * Starting qguessr filtyp 4 mr 0 * Starting qmodr * Starting qsplitr to split the file * 0 lines copied to ./1xxx.raw_dis * 1242 lines copied to ./1xxx.raw_noe * 0 lines copied to ./1xxx.raw_hb * 0 lines copied to ./1xxx.raw_ss * 0 lines copied to ./1xxx.raw_tor * 0 lines copied to ./1xxx.raw * 0 lines copied to ./1xxx.raw_mdl * 0 remaining lines Preparing for qconvr * Converting <./1xxx.raw_noe> without mrfile to <./1xxx.noe> * Conversion successful count 1242 type diana Aqua program directory: /u02/jurgen/src/aqua3.2 AQ2X - Converting distance restraints AQ2X - Project name is 1xxx_1 * Coordinate file type determined as PDB * * Processing coordinate file 1xxx_1.pdb into Aqua file * * One or more atoms could not be found in the AtomLIB * Number of structures: 1 * Number of residues: 102 * Number of atoms: 1677 * * Processing restraint file temp.all * * Read 1242 distance restraints successfully! * Distance restraints have been written AQ2X - Log file: aq2x.log == generating parameter file for xplor refinement starting waterrefine.py Reading CONFIGURATION file /u/volkman/at1g16640/9valid/7e/config/nmr_refine.conf... Reading PARAMETER file /u/volkman/at1g16640/9valid/7e/config/refine.pars... WARNING - No data found behind equals sign in /u/volkman/at1g16640/9valid/7e/config/refine.pars at COUP_FILE =. Script will continue. WARNING - No data found behind equals sign in /u/volkman/at1g16640/9valid/7e/config/refine.pars at SANI_FILE =. Script will continue. WARNING - No data found behind equals sign in /u/volkman/at1g16640/9valid/7e/config/refine.pars at VEAN_FILE =. Script will continue. Creating directory /u/volkman/at1g16640/9valid/7e/analyzed_input Found 20 structures with base filename "1xxx" Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_1.pdb Sending job 1 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_2.pdb Sending job 2 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_3.pdb Sending job 3 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_4.pdb Sending job 4 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_5.pdb Sending job 5 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_6.pdb Sending job 6 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_7.pdb Sending job 7 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_8.pdb Sending job 8 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_9.pdb Sending job 9 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_10.pdb Sending job 10 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_11.pdb Sending job 11 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_12.pdb Sending job 12 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_13.pdb Sending job 13 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_14.pdb Sending job 14 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_15.pdb Sending job 15 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_16.pdb Sending job 16 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_17.pdb Sending job 17 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_18.pdb Sending job 18 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_19.pdb Sending job 19 to the queu Starting analysis of structure /u/volkman/at1g16640/9valid/7e/input/1xxx_20.pdb Sending job 20 to the queu Done with the analysis of the input coordinate and constraints Starting protein structure checks of the analyzed input structures DEBUG: doing writing xplor file list DEBUG: done with writing xplor file list Doing the procheck validation analysis Analysis of the input structures is finished Creating directory /u/volkman/at1g16640/9valid/7e/refined_input Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_1.pdb Sending job 1 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_2.pdb Sending job 2 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_3.pdb Sending job 3 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_4.pdb Sending job 4 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_5.pdb Sending job 5 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_6.pdb Sending job 6 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_7.pdb Sending job 7 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_8.pdb Sending job 8 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_9.pdb Sending job 9 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_10.pdb Sending job 10 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_11.pdb Sending job 11 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_12.pdb Sending job 12 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_13.pdb Sending job 13 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_14.pdb Sending job 14 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_15.pdb Sending job 15 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_16.pdb Sending job 16 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_17.pdb Sending job 17 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_18.pdb Sending job 18 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_19.pdb Sending job 19 to the queu Starting refinement of structure /u/volkman/at1g16640/9valid/7e/analyzed_input/analyzed_20.pdb Sending job 20 to the queu Refinement and analysis of the input structures is finished