null Mon 24 Dec 01:05:30 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkm-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:05:36 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-mrncs/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 1181 and 0 Target number of residues in the AU: 1181 Target solvent content: 0.6199 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-3.6-parrot-mrncs.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: 19 Cell parameters: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.60 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: 75.160 3.600 Wilson plot Bfac: 61.41 20157 reflections ( 99.97 % complete ) and 0 restraints for refining 15839 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3038 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2877 (Rfree = 0.000) for 15839 atoms. Found 92 (101 requested) and removed 121 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 16149 seeds are put forward NCS extension: 0 residues added, 16149 seeds are put forward Round 1: 671 peptides, 132 chains. Longest chain 11 peptides. Score 0.323 Round 2: 905 peptides, 151 chains. Longest chain 17 peptides. Score 0.467 Round 3: 974 peptides, 146 chains. Longest chain 25 peptides. Score 0.541 Round 4: 1024 peptides, 146 chains. Longest chain 32 peptides. Score 0.578 Round 5: 1030 peptides, 137 chains. Longest chain 22 peptides. Score 0.610 Taking the results from Round 5 Chains 143, Residues 893, Estimated correctness of the model 18.5 % 12 chains (78 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29101 restraints for refining 12919 atoms. 25479 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2481 (Rfree = 0.000) for 12919 atoms. Found 63 (82 requested) and removed 97 (41 requested) atoms. Cycle 2: After refmac, R = 0.2271 (Rfree = 0.000) for 12669 atoms. Found 45 (82 requested) and removed 78 (41 requested) atoms. Cycle 3: After refmac, R = 0.2286 (Rfree = 0.000) for 12560 atoms. Found 51 (81 requested) and removed 78 (40 requested) atoms. Cycle 4: After refmac, R = 0.2171 (Rfree = 0.000) for 12492 atoms. Found 47 (80 requested) and removed 78 (40 requested) atoms. Cycle 5: After refmac, R = 0.2167 (Rfree = 0.000) for 12398 atoms. Found 45 (79 requested) and removed 67 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.61 Search for helices and strands: 0 residues in 0 chains, 12780 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 12794 seeds are put forward Round 1: 836 peptides, 144 chains. Longest chain 16 peptides. Score 0.432 Round 2: 959 peptides, 148 chains. Longest chain 20 peptides. Score 0.522 Round 3: 982 peptides, 138 chains. Longest chain 20 peptides. Score 0.573 Round 4: 978 peptides, 137 chains. Longest chain 19 peptides. Score 0.574 Round 5: 999 peptides, 141 chains. Longest chain 20 peptides. Score 0.576 Taking the results from Round 5 Chains 146, Residues 858, Estimated correctness of the model 5.1 % 12 chains (95 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 28472 restraints for refining 12691 atoms. 24936 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2219 (Rfree = 0.000) for 12691 atoms. Found 43 (81 requested) and removed 109 (40 requested) atoms. Cycle 7: After refmac, R = 0.2049 (Rfree = 0.000) for 12537 atoms. Found 30 (80 requested) and removed 68 (40 requested) atoms. Cycle 8: After refmac, R = 0.2124 (Rfree = 0.000) for 12459 atoms. Found 44 (80 requested) and removed 63 (40 requested) atoms. Cycle 9: After refmac, R = 0.2134 (Rfree = 0.000) for 12417 atoms. Found 41 (79 requested) and removed 74 (39 requested) atoms. Cycle 10: After refmac, R = 0.2112 (Rfree = 0.000) for 12353 atoms. Found 60 (79 requested) and removed 55 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.65 Search for helices and strands: 0 residues in 0 chains, 12772 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 12794 seeds are put forward Round 1: 854 peptides, 141 chains. Longest chain 18 peptides. Score 0.460 Round 2: 950 peptides, 130 chains. Longest chain 19 peptides. Score 0.576 Round 3: 939 peptides, 133 chains. Longest chain 20 peptides. Score 0.558 Round 4: 941 peptides, 121 chains. Longest chain 21 peptides. Score 0.598 Round 5: 953 peptides, 130 chains. Longest chain 20 peptides. Score 0.578 Taking the results from Round 4 Chains 127, Residues 820, Estimated correctness of the model 13.9 % 12 chains (93 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 28304 restraints for refining 12750 atoms. 24885 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2132 (Rfree = 0.000) for 12750 atoms. Found 39 (81 requested) and removed 138 (40 requested) atoms. Cycle 12: After refmac, R = 0.1976 (Rfree = 0.000) for 12583 atoms. Found 30 (81 requested) and removed 69 (40 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 12505 atoms. Found 21 (80 requested) and removed 65 (40 requested) atoms. Cycle 14: After refmac, R = 0.1915 (Rfree = 0.000) for 12445 atoms. Found 33 (79 requested) and removed 65 (39 requested) atoms. Cycle 15: After refmac, R = 0.1887 (Rfree = 0.000) for 12394 atoms. Found 23 (79 requested) and removed 57 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 12738 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 12758 seeds are put forward Round 1: 845 peptides, 143 chains. Longest chain 21 peptides. Score 0.444 Round 2: 901 peptides, 123 chains. Longest chain 26 peptides. Score 0.562 Round 3: 900 peptides, 125 chains. Longest chain 18 peptides. Score 0.555 Round 4: 919 peptides, 128 chains. Longest chain 27 peptides. Score 0.559 Round 5: 882 peptides, 121 chains. Longest chain 22 peptides. Score 0.555 Taking the results from Round 2 Chains 126, Residues 778, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 28846 restraints for refining 12652 atoms. 25766 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2078 (Rfree = 0.000) for 12652 atoms. Found 47 (81 requested) and removed 93 (40 requested) atoms. Cycle 17: After refmac, R = 0.2099 (Rfree = 0.000) for 12581 atoms. Found 43 (80 requested) and removed 77 (40 requested) atoms. Cycle 18: After refmac, R = 0.1774 (Rfree = 0.000) for 12530 atoms. Found 18 (80 requested) and removed 62 (40 requested) atoms. Cycle 19: After refmac, R = 0.1708 (Rfree = 0.000) for 12470 atoms. Found 8 (80 requested) and removed 49 (40 requested) atoms. Cycle 20: After refmac, R = 0.1689 (Rfree = 0.000) for 12425 atoms. Found 7 (79 requested) and removed 43 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 12818 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 12832 seeds are put forward Round 1: 763 peptides, 135 chains. Longest chain 16 peptides. Score 0.401 Round 2: 850 peptides, 129 chains. Longest chain 25 peptides. Score 0.501 Round 3: 875 peptides, 126 chains. Longest chain 24 peptides. Score 0.532 Round 4: 880 peptides, 121 chains. Longest chain 25 peptides. Score 0.553 Round 5: 878 peptides, 125 chains. Longest chain 17 peptides. Score 0.538 Taking the results from Round 4 Chains 122, Residues 759, Estimated correctness of the model 0.0 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29361 restraints for refining 12870 atoms. 26322 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2013 (Rfree = 0.000) for 12870 atoms. Found 33 (82 requested) and removed 100 (41 requested) atoms. Cycle 22: After refmac, R = 0.1939 (Rfree = 0.000) for 12759 atoms. Found 41 (82 requested) and removed 69 (41 requested) atoms. Cycle 23: After refmac, R = 0.1942 (Rfree = 0.000) for 12701 atoms. Found 54 (81 requested) and removed 64 (40 requested) atoms. Cycle 24: After refmac, R = 0.1823 (Rfree = 0.000) for 12673 atoms. Found 31 (81 requested) and removed 56 (40 requested) atoms. Cycle 25: After refmac, R = 0.1549 (Rfree = 0.000) for 12637 atoms. Found 14 (81 requested) and removed 53 (40 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 12986 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 13010 seeds are put forward Round 1: 755 peptides, 139 chains. Longest chain 16 peptides. Score 0.377 Round 2: 815 peptides, 123 chains. Longest chain 18 peptides. Score 0.493 Round 3: 835 peptides, 122 chains. Longest chain 20 peptides. Score 0.514 Round 4: 832 peptides, 123 chains. Longest chain 18 peptides. Score 0.508 Round 5: 833 peptides, 112 chains. Longest chain 30 peptides. Score 0.548 Taking the results from Round 5 Chains 114, Residues 721, Estimated correctness of the model 0.0 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29642 restraints for refining 12923 atoms. 26743 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2024 (Rfree = 0.000) for 12923 atoms. Found 43 (82 requested) and removed 74 (41 requested) atoms. Cycle 27: After refmac, R = 0.1932 (Rfree = 0.000) for 12848 atoms. Found 50 (82 requested) and removed 70 (41 requested) atoms. Cycle 28: After refmac, R = 0.1895 (Rfree = 0.000) for 12807 atoms. Found 40 (82 requested) and removed 62 (41 requested) atoms. Cycle 29: After refmac, R = 0.1854 (Rfree = 0.000) for 12765 atoms. Found 45 (82 requested) and removed 60 (41 requested) atoms. Cycle 30: After refmac, R = 0.1563 (Rfree = 0.000) for 12739 atoms. Found 9 (81 requested) and removed 47 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 13078 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 13102 seeds are put forward Round 1: 683 peptides, 132 chains. Longest chain 19 peptides. Score 0.335 Round 2: 761 peptides, 124 chains. Longest chain 18 peptides. Score 0.442 Round 3: 815 peptides, 128 chains. Longest chain 16 peptides. Score 0.475 Round 4: 805 peptides, 128 chains. Longest chain 17 peptides. Score 0.466 Round 5: 820 peptides, 128 chains. Longest chain 17 peptides. Score 0.479 Taking the results from Round 5 Chains 130, Residues 692, Estimated correctness of the model 0.0 % 9 chains (63 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29519 restraints for refining 12924 atoms. 26706 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1928 (Rfree = 0.000) for 12924 atoms. Found 50 (82 requested) and removed 75 (41 requested) atoms. Cycle 32: After refmac, R = 0.1889 (Rfree = 0.000) for 12848 atoms. Found 48 (82 requested) and removed 54 (41 requested) atoms. Cycle 33: After refmac, R = 0.1830 (Rfree = 0.000) for 12806 atoms. Found 42 (82 requested) and removed 57 (41 requested) atoms. Cycle 34: After refmac, R = 0.1513 (Rfree = 0.000) for 12769 atoms. Found 9 (82 requested) and removed 48 (41 requested) atoms. Cycle 35: After refmac, R = 0.1452 (Rfree = 0.000) for 12724 atoms. Found 9 (81 requested) and removed 42 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 13052 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 13073 seeds are put forward Round 1: 607 peptides, 120 chains. Longest chain 15 peptides. Score 0.309 Round 2: 701 peptides, 121 chains. Longest chain 15 peptides. Score 0.399 Round 3: 716 peptides, 117 chains. Longest chain 17 peptides. Score 0.429 Round 4: 718 peptides, 114 chains. Longest chain 15 peptides. Score 0.443 Round 5: 744 peptides, 118 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 5 Chains 119, Residues 626, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29816 restraints for refining 12924 atoms. 27334 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1866 (Rfree = 0.000) for 12924 atoms. Found 44 (82 requested) and removed 77 (41 requested) atoms. Cycle 37: After refmac, R = 0.1884 (Rfree = 0.000) for 12851 atoms. Found 48 (82 requested) and removed 62 (41 requested) atoms. Cycle 38: After refmac, R = 0.1851 (Rfree = 0.000) for 12817 atoms. Found 50 (82 requested) and removed 61 (41 requested) atoms. Cycle 39: After refmac, R = 0.1832 (Rfree = 0.000) for 12793 atoms. Found 39 (82 requested) and removed 54 (41 requested) atoms. Cycle 40: After refmac, R = 0.1542 (Rfree = 0.000) for 12768 atoms. Found 11 (81 requested) and removed 43 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 13094 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 13105 seeds are put forward Round 1: 612 peptides, 121 chains. Longest chain 11 peptides. Score 0.310 Round 2: 667 peptides, 112 chains. Longest chain 15 peptides. Score 0.403 Round 3: 682 peptides, 113 chains. Longest chain 18 peptides. Score 0.413 Round 4: 680 peptides, 110 chains. Longest chain 15 peptides. Score 0.424 Round 5: 675 peptides, 109 chains. Longest chain 14 peptides. Score 0.423 Taking the results from Round 4 Chains 110, Residues 570, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 30584 restraints for refining 12923 atoms. 28384 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1847 (Rfree = 0.000) for 12923 atoms. Found 30 (82 requested) and removed 52 (41 requested) atoms. Cycle 42: After refmac, R = 0.1790 (Rfree = 0.000) for 12861 atoms. Found 56 (82 requested) and removed 51 (41 requested) atoms. Cycle 43: After refmac, R = 0.1815 (Rfree = 0.000) for 12850 atoms. Found 48 (82 requested) and removed 57 (41 requested) atoms. Cycle 44: After refmac, R = 0.1761 (Rfree = 0.000) for 12829 atoms. Found 59 (82 requested) and removed 54 (41 requested) atoms. Cycle 45: After refmac, R = 0.1460 (Rfree = 0.000) for 12827 atoms. Found 11 (82 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.61 Search for helices and strands: 0 residues in 0 chains, 13185 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 13197 seeds are put forward Round 1: 525 peptides, 108 chains. Longest chain 10 peptides. Score 0.275 Round 2: 644 peptides, 117 chains. Longest chain 15 peptides. Score 0.360 Round 3: 631 peptides, 110 chains. Longest chain 13 peptides. Score 0.377 Round 4: 631 peptides, 106 chains. Longest chain 20 peptides. Score 0.394 Round 5: 622 peptides, 107 chains. Longest chain 18 peptides. Score 0.381 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 108, Residues 525, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 108 chains (525 residues) following loop building 6 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20157 reflections ( 99.97 % complete ) and 30525 restraints for refining 12924 atoms. 28460 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1835 (Rfree = 0.000) for 12924 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 47: After refmac, R = 0.1831 (Rfree = 0.000) for 12864 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1821 (Rfree = 0.000) for 12817 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 49: After refmac, R = 0.1775 (Rfree = 0.000) for 12769 atoms. Found 0 (81 requested) and removed 40 (40 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:27:42 GMT 2018 Job finished. TimeTaking 142.2 Used memory is bytes: 24259816