null Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ash-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1112 and 0 Target number of residues in the AU: 1112 Target solvent content: 0.6577 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 103.605 3.600 Wilson plot Bfac: 83.27 20233 reflections ( 99.76 % complete ) and 0 restraints for refining 13430 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3343 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2846 (Rfree = 0.000) for 13430 atoms. Found 86 (86 requested) and removed 77 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 13698 seeds are put forward NCS extension: 0 residues added, 13698 seeds are put forward Round 1: 617 peptides, 118 chains. Longest chain 13 peptides. Score 0.323 Round 2: 786 peptides, 124 chains. Longest chain 18 peptides. Score 0.455 Round 3: 841 peptides, 119 chains. Longest chain 17 peptides. Score 0.518 Round 4: 867 peptides, 118 chains. Longest chain 17 peptides. Score 0.542 Round 5: 841 peptides, 113 chains. Longest chain 19 peptides. Score 0.539 Taking the results from Round 4 Chains 120, Residues 749, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 24990 restraints for refining 11049 atoms. 21958 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2425 (Rfree = 0.000) for 11049 atoms. Found 70 (70 requested) and removed 77 (35 requested) atoms. Cycle 2: After refmac, R = 0.2201 (Rfree = 0.000) for 10888 atoms. Found 34 (70 requested) and removed 65 (35 requested) atoms. Cycle 3: After refmac, R = 0.2141 (Rfree = 0.000) for 10782 atoms. Found 31 (69 requested) and removed 40 (34 requested) atoms. Cycle 4: After refmac, R = 0.2124 (Rfree = 0.000) for 10716 atoms. Found 29 (69 requested) and removed 53 (34 requested) atoms. Cycle 5: After refmac, R = 0.2080 (Rfree = 0.000) for 10654 atoms. Found 24 (68 requested) and removed 43 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11029 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11049 seeds are put forward Round 1: 756 peptides, 129 chains. Longest chain 15 peptides. Score 0.410 Round 2: 857 peptides, 120 chains. Longest chain 20 peptides. Score 0.527 Round 3: 863 peptides, 114 chains. Longest chain 21 peptides. Score 0.552 Round 4: 870 peptides, 117 chains. Longest chain 22 peptides. Score 0.547 Round 5: 871 peptides, 109 chains. Longest chain 24 peptides. Score 0.575 Taking the results from Round 5 Chains 115, Residues 762, Estimated correctness of the model 4.6 % 9 chains (75 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 24314 restraints for refining 11048 atoms. 21120 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2275 (Rfree = 0.000) for 11048 atoms. Found 51 (70 requested) and removed 62 (35 requested) atoms. Cycle 7: After refmac, R = 0.2087 (Rfree = 0.000) for 10967 atoms. Found 27 (70 requested) and removed 49 (35 requested) atoms. Cycle 8: After refmac, R = 0.2040 (Rfree = 0.000) for 10912 atoms. Found 22 (70 requested) and removed 43 (35 requested) atoms. Cycle 9: After refmac, R = 0.1998 (Rfree = 0.000) for 10877 atoms. Found 11 (69 requested) and removed 37 (34 requested) atoms. Cycle 10: After refmac, R = 0.1969 (Rfree = 0.000) for 10843 atoms. Found 10 (69 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 11172 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 11203 seeds are put forward Round 1: 766 peptides, 130 chains. Longest chain 20 peptides. Score 0.415 Round 2: 853 peptides, 115 chains. Longest chain 21 peptides. Score 0.541 Round 3: 851 peptides, 114 chains. Longest chain 25 peptides. Score 0.543 Round 4: 852 peptides, 118 chains. Longest chain 22 peptides. Score 0.530 Round 5: 835 peptides, 104 chains. Longest chain 26 peptides. Score 0.565 Taking the results from Round 5 Chains 113, Residues 731, Estimated correctness of the model 0.5 % 9 chains (130 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 23788 restraints for refining 11052 atoms. 20445 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2262 (Rfree = 0.000) for 11052 atoms. Found 68 (70 requested) and removed 84 (35 requested) atoms. Cycle 12: After refmac, R = 0.2064 (Rfree = 0.000) for 10981 atoms. Found 23 (70 requested) and removed 50 (35 requested) atoms. Cycle 13: After refmac, R = 0.2031 (Rfree = 0.000) for 10920 atoms. Found 24 (70 requested) and removed 44 (35 requested) atoms. Cycle 14: After refmac, R = 0.1990 (Rfree = 0.000) for 10881 atoms. Found 15 (69 requested) and removed 44 (34 requested) atoms. Cycle 15: After refmac, R = 0.1956 (Rfree = 0.000) for 10822 atoms. Found 29 (69 requested) and removed 43 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11182 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 11212 seeds are put forward Round 1: 703 peptides, 124 chains. Longest chain 18 peptides. Score 0.381 Round 2: 795 peptides, 116 chains. Longest chain 25 peptides. Score 0.492 Round 3: 817 peptides, 114 chains. Longest chain 22 peptides. Score 0.517 Round 4: 831 peptides, 110 chains. Longest chain 23 peptides. Score 0.542 Round 5: 836 peptides, 112 chains. Longest chain 22 peptides. Score 0.539 Taking the results from Round 4 Chains 111, Residues 721, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 24957 restraints for refining 11052 atoms. 22130 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2081 (Rfree = 0.000) for 11052 atoms. Found 52 (70 requested) and removed 46 (35 requested) atoms. Cycle 17: After refmac, R = 0.1902 (Rfree = 0.000) for 10978 atoms. Found 20 (70 requested) and removed 43 (35 requested) atoms. Cycle 18: After refmac, R = 0.1857 (Rfree = 0.000) for 10925 atoms. Found 17 (70 requested) and removed 35 (35 requested) atoms. Cycle 19: After refmac, R = 0.1837 (Rfree = 0.000) for 10895 atoms. Found 8 (69 requested) and removed 37 (34 requested) atoms. Cycle 20: After refmac, R = 0.1826 (Rfree = 0.000) for 10862 atoms. Found 10 (69 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11210 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 11223 seeds are put forward Round 1: 746 peptides, 123 chains. Longest chain 15 peptides. Score 0.424 Round 2: 809 peptides, 115 chains. Longest chain 19 peptides. Score 0.507 Round 3: 797 peptides, 112 chains. Longest chain 19 peptides. Score 0.508 Round 4: 827 peptides, 118 chains. Longest chain 26 peptides. Score 0.511 Round 5: 818 peptides, 115 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 5 Chains 118, Residues 703, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25247 restraints for refining 11048 atoms. 22439 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2063 (Rfree = 0.000) for 11048 atoms. Found 45 (70 requested) and removed 47 (35 requested) atoms. Cycle 22: After refmac, R = 0.1915 (Rfree = 0.000) for 11005 atoms. Found 17 (70 requested) and removed 40 (35 requested) atoms. Cycle 23: After refmac, R = 0.1875 (Rfree = 0.000) for 10971 atoms. Found 14 (70 requested) and removed 37 (35 requested) atoms. Cycle 24: After refmac, R = 0.1859 (Rfree = 0.000) for 10942 atoms. Found 10 (70 requested) and removed 37 (35 requested) atoms. Cycle 25: After refmac, R = 0.1836 (Rfree = 0.000) for 10910 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11243 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 11253 seeds are put forward Round 1: 712 peptides, 126 chains. Longest chain 16 peptides. Score 0.381 Round 2: 741 peptides, 115 chains. Longest chain 18 peptides. Score 0.450 Round 3: 744 peptides, 106 chains. Longest chain 20 peptides. Score 0.487 Round 4: 717 peptides, 108 chains. Longest chain 21 peptides. Score 0.456 Round 5: 756 peptides, 110 chains. Longest chain 22 peptides. Score 0.482 Taking the results from Round 3 Chains 106, Residues 638, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25728 restraints for refining 11051 atoms. 23210 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1960 (Rfree = 0.000) for 11051 atoms. Found 34 (70 requested) and removed 49 (35 requested) atoms. Cycle 27: After refmac, R = 0.1834 (Rfree = 0.000) for 10998 atoms. Found 21 (70 requested) and removed 41 (35 requested) atoms. Cycle 28: After refmac, R = 0.1884 (Rfree = 0.000) for 10954 atoms. Found 13 (70 requested) and removed 39 (35 requested) atoms. Cycle 29: After refmac, R = 0.1973 (Rfree = 0.000) for 10908 atoms. Found 66 (70 requested) and removed 45 (35 requested) atoms. Cycle 30: After refmac, R = 0.1971 (Rfree = 0.000) for 10909 atoms. Found 48 (70 requested) and removed 46 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11308 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 11322 seeds are put forward Round 1: 651 peptides, 125 chains. Longest chain 22 peptides. Score 0.327 Round 2: 732 peptides, 122 chains. Longest chain 15 peptides. Score 0.415 Round 3: 719 peptides, 109 chains. Longest chain 17 peptides. Score 0.454 Round 4: 733 peptides, 115 chains. Longest chain 15 peptides. Score 0.443 Round 5: 743 peptides, 110 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 5 Chains 110, Residues 633, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25764 restraints for refining 11051 atoms. 23289 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2036 (Rfree = 0.000) for 11051 atoms. Found 64 (70 requested) and removed 47 (35 requested) atoms. Cycle 32: After refmac, R = 0.1933 (Rfree = 0.000) for 11019 atoms. Found 43 (71 requested) and removed 38 (35 requested) atoms. Cycle 33: After refmac, R = 0.1907 (Rfree = 0.000) for 10991 atoms. Found 46 (70 requested) and removed 44 (35 requested) atoms. Cycle 34: After refmac, R = 0.1873 (Rfree = 0.000) for 10971 atoms. Found 66 (70 requested) and removed 44 (35 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 10973 atoms. Found 70 (70 requested) and removed 46 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 11339 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11356 seeds are put forward Round 1: 602 peptides, 117 chains. Longest chain 12 peptides. Score 0.312 Round 2: 717 peptides, 123 chains. Longest chain 19 peptides. Score 0.398 Round 3: 726 peptides, 114 chains. Longest chain 20 peptides. Score 0.441 Round 4: 741 peptides, 113 chains. Longest chain 17 peptides. Score 0.458 Round 5: 741 peptides, 110 chains. Longest chain 19 peptides. Score 0.469 Taking the results from Round 5 Chains 110, Residues 631, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25738 restraints for refining 11048 atoms. 23324 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1966 (Rfree = 0.000) for 11048 atoms. Found 50 (70 requested) and removed 37 (35 requested) atoms. Cycle 37: After refmac, R = 0.1928 (Rfree = 0.000) for 11003 atoms. Found 44 (70 requested) and removed 48 (35 requested) atoms. Cycle 38: After refmac, R = 0.1894 (Rfree = 0.000) for 10979 atoms. Found 42 (70 requested) and removed 45 (35 requested) atoms. Cycle 39: After refmac, R = 0.1863 (Rfree = 0.000) for 10953 atoms. Found 47 (70 requested) and removed 42 (35 requested) atoms. Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 10943 atoms. Found 49 (70 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11382 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 11395 seeds are put forward Round 1: 539 peptides, 110 chains. Longest chain 12 peptides. Score 0.278 Round 2: 676 peptides, 114 chains. Longest chain 18 peptides. Score 0.396 Round 3: 683 peptides, 110 chains. Longest chain 16 peptides. Score 0.419 Round 4: 668 peptides, 106 chains. Longest chain 19 peptides. Score 0.421 Round 5: 672 peptides, 108 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 4 Chains 106, Residues 562, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 26179 restraints for refining 11051 atoms. 24037 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1999 (Rfree = 0.000) for 11051 atoms. Found 64 (70 requested) and removed 38 (35 requested) atoms. Cycle 42: After refmac, R = 0.1936 (Rfree = 0.000) for 11039 atoms. Found 67 (71 requested) and removed 38 (35 requested) atoms. Cycle 43: After refmac, R = 0.1936 (Rfree = 0.000) for 11042 atoms. Found 47 (71 requested) and removed 40 (35 requested) atoms. Cycle 44: After refmac, R = 0.1860 (Rfree = 0.000) for 11040 atoms. Found 45 (70 requested) and removed 43 (35 requested) atoms. Cycle 45: After refmac, R = 0.1909 (Rfree = 0.000) for 11030 atoms. Found 55 (70 requested) and removed 45 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 11413 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 11443 seeds are put forward Round 1: 513 peptides, 105 chains. Longest chain 10 peptides. Score 0.272 Round 2: 624 peptides, 107 chains. Longest chain 13 peptides. Score 0.376 Round 3: 619 peptides, 105 chains. Longest chain 20 peptides. Score 0.379 Round 4: 632 peptides, 99 chains. Longest chain 17 peptides. Score 0.416 Round 5: 637 peptides, 102 chains. Longest chain 19 peptides. Score 0.409 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 99, Residues 533, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20233 reflections ( 99.76 % complete ) and 26192 restraints for refining 11051 atoms. 24159 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1932 (Rfree = 0.000) for 11051 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.1854 (Rfree = 0.000) for 10970 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1849 (Rfree = 0.000) for 10917 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1774 (Rfree = 0.000) for 10866 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:35:42 GMT 2018 Job finished. TimeTaking 132.78 Used memory is bytes: 19852104