Sun 23 Dec 22:23:08 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 2okf-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okf-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okf-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-1.6-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/2okf-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-1.6-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 22:23:17 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/2okf-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-1.6-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 309 and 0 Target number of residues in the AU: 309 Target solvent content: 0.4483 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 280 Adjusted target solvent content: 0.50 Input MTZ file: 2okf-1.6-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: 144 Cell parameters: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2240 target number of atoms Had to go as low as 0.35 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 1 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: 27.710 1.600 Wilson plot Bfac: 14.35 38581 reflections ( 99.60 % complete ) and 0 restraints for refining 2465 atoms. Observations/parameters ratio is 3.91 ------------------------------------------------------ Starting model: R = 0.3024 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2496 (Rfree = 0.000) for 2465 atoms. Found 136 (159 requested) and removed 87 (79 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.67 1.67 NCS extension: 0 residues added, 2514 seeds are put forward Round 1: 216 peptides, 12 chains. Longest chain 64 peptides. Score 0.850 Round 2: 224 peptides, 8 chains. Longest chain 73 peptides. Score 0.894 Round 3: 225 peptides, 8 chains. Longest chain 71 peptides. Score 0.895 Round 4: 226 peptides, 7 chains. Longest chain 73 peptides. Score 0.904 Round 5: 226 peptides, 9 chains. Longest chain 71 peptides. Score 0.889 Taking the results from Round 4 Chains 8, Residues 219, Estimated correctness of the model 99.5 % 6 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 70 A Built loop between residues 62 B and 68 B 5 chains (230 residues) following loop building 4 chains (226 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2471 restraints for refining 2274 atoms. 556 conditional restraints added. Observations/parameters ratio is 4.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2570 (Rfree = 0.000) for 2274 atoms. Found 90 (147 requested) and removed 34 (73 requested) atoms. Cycle 2: After refmac, R = 0.2398 (Rfree = 0.000) for 2329 atoms. Found 75 (150 requested) and removed 12 (75 requested) atoms. Cycle 3: After refmac, R = 0.2181 (Rfree = 0.000) for 2387 atoms. Found 74 (154 requested) and removed 7 (77 requested) atoms. Cycle 4: After refmac, R = 0.2074 (Rfree = 0.000) for 2451 atoms. Found 63 (158 requested) and removed 16 (79 requested) atoms. Cycle 5: After refmac, R = 0.2006 (Rfree = 0.000) for 2493 atoms. Found 51 (161 requested) and removed 8 (80 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.62 1.62 NCS extension: 0 residues added, 2537 seeds are put forward Round 1: 236 peptides, 8 chains. Longest chain 73 peptides. Score 0.907 Round 2: 235 peptides, 9 chains. Longest chain 74 peptides. Score 0.900 Round 3: 233 peptides, 9 chains. Longest chain 73 peptides. Score 0.897 Round 4: 235 peptides, 8 chains. Longest chain 74 peptides. Score 0.906 Round 5: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Taking the results from Round 5 Chains 7, Residues 232, Estimated correctness of the model 99.6 % 5 chains (225 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 67 A 6 chains (234 residues) following loop building 4 chains (227 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2545 restraints for refining 2397 atoms. 611 conditional restraints added. Observations/parameters ratio is 4.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2068 (Rfree = 0.000) for 2397 atoms. Found 113 (155 requested) and removed 25 (77 requested) atoms. Cycle 7: After refmac, R = 0.2013 (Rfree = 0.000) for 2481 atoms. Found 66 (160 requested) and removed 15 (80 requested) atoms. Cycle 8: After refmac, R = 0.1944 (Rfree = 0.000) for 2527 atoms. Found 69 (163 requested) and removed 9 (81 requested) atoms. Cycle 9: After refmac, R = 0.1907 (Rfree = 0.000) for 2585 atoms. Found 53 (167 requested) and removed 15 (83 requested) atoms. Cycle 10: After refmac, R = 0.1874 (Rfree = 0.000) for 2619 atoms. Found 55 (169 requested) and removed 12 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.62 1.62 NCS extension: 0 residues added, 2662 seeds are put forward Round 1: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Round 2: 238 peptides, 9 chains. Longest chain 62 peptides. Score 0.903 Round 3: 237 peptides, 5 chains. Longest chain 96 peptides. Score 0.927 Round 4: 238 peptides, 9 chains. Longest chain 62 peptides. Score 0.903 Round 5: 236 peptides, 5 chains. Longest chain 95 peptides. Score 0.926 Taking the results from Round 3 Chains 6, Residues 232, Estimated correctness of the model 99.7 % 4 chains (227 residues) have been docked in sequence Building loops using Loopy2018 6 chains (232 residues) following loop building 4 chains (227 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2663 restraints for refining 2491 atoms. 737 conditional restraints added. Observations/parameters ratio is 3.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1982 (Rfree = 0.000) for 2491 atoms. Found 122 (161 requested) and removed 27 (80 requested) atoms. Cycle 12: After refmac, R = 0.1967 (Rfree = 0.000) for 2580 atoms. Found 67 (167 requested) and removed 22 (83 requested) atoms. Cycle 13: After refmac, R = 0.1922 (Rfree = 0.000) for 2624 atoms. Found 57 (169 requested) and removed 14 (84 requested) atoms. Cycle 14: After refmac, R = 0.1885 (Rfree = 0.000) for 2659 atoms. Found 50 (172 requested) and removed 15 (86 requested) atoms. Cycle 15: After refmac, R = 0.1846 (Rfree = 0.000) for 2692 atoms. Found 52 (174 requested) and removed 20 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.61 1.61 NCS extension: 2 residues added (93 deleted due to clashes), 2727 seeds are put forward Round 1: 236 peptides, 5 chains. Longest chain 95 peptides. Score 0.926 Round 2: 231 peptides, 7 chains. Longest chain 73 peptides. Score 0.909 Round 3: 234 peptides, 6 chains. Longest chain 95 peptides. Score 0.918 Round 4: 236 peptides, 5 chains. Longest chain 95 peptides. Score 0.926 Round 5: 234 peptides, 6 chains. Longest chain 95 peptides. Score 0.918 Taking the results from Round 4 Chains 5, Residues 231, Estimated correctness of the model 99.7 % 4 chains (227 residues) have been docked in sequence Building loops using Loopy2018 5 chains (231 residues) following loop building 4 chains (227 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2741 restraints for refining 2544 atoms. 818 conditional restraints added. Observations/parameters ratio is 3.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1956 (Rfree = 0.000) for 2544 atoms. Found 108 (164 requested) and removed 24 (82 requested) atoms. Cycle 17: After refmac, R = 0.1921 (Rfree = 0.000) for 2622 atoms. Found 78 (170 requested) and removed 21 (85 requested) atoms. Cycle 18: After refmac, R = 0.1871 (Rfree = 0.000) for 2676 atoms. Found 59 (173 requested) and removed 9 (86 requested) atoms. Cycle 19: After refmac, R = 0.1849 (Rfree = 0.000) for 2721 atoms. Found 43 (176 requested) and removed 20 (88 requested) atoms. Cycle 20: After refmac, R = 0.1812 (Rfree = 0.000) for 2734 atoms. Found 62 (177 requested) and removed 23 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.62 1.62 NCS extension: 1 residues added (94 deleted due to clashes), 2776 seeds are put forward Round 1: 234 peptides, 6 chains. Longest chain 95 peptides. Score 0.918 Round 2: 236 peptides, 5 chains. Longest chain 95 peptides. Score 0.926 Round 3: 232 peptides, 7 chains. Longest chain 95 peptides. Score 0.910 Round 4: 231 peptides, 8 chains. Longest chain 73 peptides. Score 0.902 Round 5: 232 peptides, 7 chains. Longest chain 95 peptides. Score 0.910 Taking the results from Round 2 Chains 5, Residues 231, Estimated correctness of the model 99.7 % 4 chains (227 residues) have been docked in sequence Building loops using Loopy2018 5 chains (231 residues) following loop building 4 chains (227 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2759 restraints for refining 2570 atoms. 836 conditional restraints added. Observations/parameters ratio is 3.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1940 (Rfree = 0.000) for 2570 atoms. Found 133 (166 requested) and removed 26 (83 requested) atoms. Cycle 22: After refmac, R = 0.1935 (Rfree = 0.000) for 2672 atoms. Found 71 (173 requested) and removed 24 (86 requested) atoms. Cycle 23: After refmac, R = 0.1899 (Rfree = 0.000) for 2712 atoms. Found 77 (175 requested) and removed 15 (87 requested) atoms. Cycle 24: After refmac, R = 0.1865 (Rfree = 0.000) for 2769 atoms. Found 72 (179 requested) and removed 24 (89 requested) atoms. Cycle 25: After refmac, R = 0.1843 (Rfree = 0.000) for 2810 atoms. Found 60 (182 requested) and removed 20 (91 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.62 1.62 NCS extension: 0 residues added, 2850 seeds are put forward Round 1: 235 peptides, 6 chains. Longest chain 95 peptides. Score 0.919 Round 2: 235 peptides, 6 chains. Longest chain 95 peptides. Score 0.919 Round 3: 234 peptides, 7 chains. Longest chain 95 peptides. Score 0.912 Round 4: 237 peptides, 5 chains. Longest chain 95 peptides. Score 0.927 Round 5: 236 peptides, 6 chains. Longest chain 95 peptides. Score 0.920 Taking the results from Round 4 Chains 5, Residues 232, Estimated correctness of the model 99.7 % 4 chains (227 residues) have been docked in sequence Building loops using Loopy2018 5 chains (232 residues) following loop building 4 chains (227 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2797 restraints for refining 2595 atoms. 870 conditional restraints added. Observations/parameters ratio is 3.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1961 (Rfree = 0.000) for 2595 atoms. Found 153 (167 requested) and removed 29 (83 requested) atoms. Cycle 27: After refmac, R = 0.1953 (Rfree = 0.000) for 2714 atoms. Found 74 (175 requested) and removed 24 (87 requested) atoms. Cycle 28: After refmac, R = 0.1893 (Rfree = 0.000) for 2761 atoms. Found 53 (178 requested) and removed 27 (89 requested) atoms. Cycle 29: After refmac, R = 0.1855 (Rfree = 0.000) for 2776 atoms. Found 64 (176 requested) and removed 19 (90 requested) atoms. Cycle 30: After refmac, R = 0.1823 (Rfree = 0.000) for 2818 atoms. Found 63 (178 requested) and removed 23 (91 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.62 1.62 NCS extension: 1 residues added (19 deleted due to clashes), 2861 seeds are put forward Round 1: 237 peptides, 7 chains. Longest chain 95 peptides. Score 0.915 Round 2: 239 peptides, 6 chains. Longest chain 95 peptides. Score 0.923 Round 3: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Round 4: 240 peptides, 6 chains. Longest chain 95 peptides. Score 0.924 Round 5: 241 peptides, 6 chains. Longest chain 95 peptides. Score 0.925 Taking the results from Round 5 Chains 6, Residues 235, Estimated correctness of the model 99.7 % 4 chains (226 residues) have been docked in sequence Building loops using Loopy2018 6 chains (235 residues) following loop building 4 chains (226 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2804 restraints for refining 2614 atoms. 870 conditional restraints added. Observations/parameters ratio is 3.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1968 (Rfree = 0.000) for 2614 atoms. Found 166 (166 requested) and removed 29 (84 requested) atoms. Cycle 32: After refmac, R = 0.1954 (Rfree = 0.000) for 2744 atoms. Found 76 (174 requested) and removed 22 (89 requested) atoms. Cycle 33: After refmac, R = 0.1892 (Rfree = 0.000) for 2790 atoms. Found 64 (177 requested) and removed 21 (90 requested) atoms. Cycle 34: After refmac, R = 0.1859 (Rfree = 0.000) for 2828 atoms. Found 64 (179 requested) and removed 18 (91 requested) atoms. Cycle 35: After refmac, R = 0.1826 (Rfree = 0.000) for 2865 atoms. Found 60 (181 requested) and removed 26 (92 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.62 1.62 NCS extension: 72 residues added (3 deleted due to clashes), 2971 seeds are put forward Round 1: 239 peptides, 6 chains. Longest chain 95 peptides. Score 0.923 Round 2: 239 peptides, 6 chains. Longest chain 95 peptides. Score 0.923 Round 3: 240 peptides, 6 chains. Longest chain 95 peptides. Score 0.924 Round 4: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Round 5: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Taking the results from Round 3 Chains 6, Residues 234, Estimated correctness of the model 99.7 % 4 chains (226 residues) have been docked in sequence Building loops using Loopy2018 6 chains (234 residues) following loop building 4 chains (226 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2888 restraints for refining 2653 atoms. 958 conditional restraints added. Observations/parameters ratio is 3.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1973 (Rfree = 0.000) for 2653 atoms. Found 156 (168 requested) and removed 36 (85 requested) atoms. Cycle 37: After refmac, R = 0.1953 (Rfree = 0.000) for 2760 atoms. Found 78 (175 requested) and removed 22 (89 requested) atoms. Cycle 38: After refmac, R = 0.1891 (Rfree = 0.000) for 2802 atoms. Found 74 (178 requested) and removed 16 (91 requested) atoms. Cycle 39: After refmac, R = 0.1854 (Rfree = 0.000) for 2853 atoms. Found 63 (181 requested) and removed 15 (92 requested) atoms. Cycle 40: After refmac, R = 0.1821 (Rfree = 0.000) for 2886 atoms. Found 41 (183 requested) and removed 24 (93 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.62 1.62 NCS extension: 0 residues added (95 deleted due to clashes), 2904 seeds are put forward Round 1: 234 peptides, 8 chains. Longest chain 73 peptides. Score 0.905 Round 2: 239 peptides, 8 chains. Longest chain 95 peptides. Score 0.910 Round 3: 240 peptides, 6 chains. Longest chain 95 peptides. Score 0.924 Round 4: 234 peptides, 8 chains. Longest chain 73 peptides. Score 0.905 Round 5: 238 peptides, 8 chains. Longest chain 62 peptides. Score 0.909 Taking the results from Round 3 Chains 7, Residues 234, Estimated correctness of the model 99.7 % 5 chains (230 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 B and 32 B Built loop between residues 35 B and 46 B 5 chains (250 residues) following loop building 3 chains (246 residues) in sequence following loop building ------------------------------------------------------ 38581 reflections ( 99.60 % complete ) and 2884 restraints for refining 2751 atoms. 828 conditional restraints added. Observations/parameters ratio is 3.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2067 (Rfree = 0.000) for 2751 atoms. Found 130 (171 requested) and removed 69 (89 requested) atoms. Cycle 42: After refmac, R = 0.1960 (Rfree = 0.000) for 2798 atoms. Found 77 (170 requested) and removed 22 (90 requested) atoms. Cycle 43: After refmac, R = 0.1883 (Rfree = 0.000) for 2847 atoms. Found 53 (173 requested) and removed 10 (92 requested) atoms. Cycle 44: After refmac, R = 0.1828 (Rfree = 0.000) for 2884 atoms. Found 55 (176 requested) and removed 17 (93 requested) atoms. Cycle 45: After refmac, R = 0.1793 (Rfree = 0.000) for 2912 atoms. Found 60 (178 requested) and removed 24 (94 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.62 1.62 NCS extension: 71 residues added (4 deleted due to clashes), 3023 seeds are put forward Round 1: 237 peptides, 8 chains. Longest chain 87 peptides. Score 0.908 Round 2: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Round 3: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Round 4: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.917 Round 5: 239 peptides, 6 chains. Longest chain 95 peptides. Score 0.923 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 233, Estimated correctness of the model 99.7 % 5 chains (226 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 21 A and 32 A Built loop between residues 35 A and 46 A 4 chains (249 residues) following loop building 3 chains (246 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38581 reflections ( 99.60 % complete ) and 2053 restraints for refining 2014 atoms. Observations/parameters ratio is 4.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2704 (Rfree = 0.000) for 2014 atoms. Found 79 (122 requested) and removed 0 (122 requested) atoms. Cycle 47: After refmac, R = 0.2438 (Rfree = 0.000) for 2014 atoms. Found 34 (127 requested) and removed 0 (67 requested) atoms. Cycle 48: After refmac, R = 0.2242 (Rfree = 0.000) for 2014 atoms. Found 20 (129 requested) and removed 1 (68 requested) atoms. Cycle 49: After refmac, R = 0.2133 (Rfree = 0.000) for 2014 atoms. TimeTaking 55.85