null Mon 24 Dec 00:06:05 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-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 00:06:09 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-4.0-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 1100 and 0 Target number of residues in the AU: 1100 Target solvent content: 0.6460 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-4.0-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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.65 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 4.000 Wilson plot Bfac: 75.51 14774 reflections ( 99.96 % complete ) and 0 restraints for refining 15785 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3229 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3111 (Rfree = 0.000) for 15785 atoms. Found 65 (75 requested) and removed 107 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 4.09 Search for helices and strands: 0 residues in 0 chains, 16077 seeds are put forward NCS extension: 0 residues added, 16077 seeds are put forward Round 1: 573 peptides, 124 chains. Longest chain 9 peptides. Score 0.254 Round 2: 743 peptides, 132 chains. Longest chain 14 peptides. Score 0.394 Round 3: 838 peptides, 139 chains. Longest chain 21 peptides. Score 0.453 Round 4: 870 peptides, 132 chains. Longest chain 15 peptides. Score 0.506 Round 5: 925 peptides, 130 chains. Longest chain 22 peptides. Score 0.557 Taking the results from Round 5 Chains 133, Residues 795, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 30425 restraints for refining 12868 atoms. 27274 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2785 (Rfree = 0.000) for 12868 atoms. Found 28 (61 requested) and removed 105 (30 requested) atoms. Cycle 2: After refmac, R = 0.2492 (Rfree = 0.000) for 12516 atoms. Found 26 (60 requested) and removed 84 (30 requested) atoms. Cycle 3: After refmac, R = 0.2310 (Rfree = 0.000) for 12303 atoms. Found 16 (59 requested) and removed 68 (29 requested) atoms. Cycle 4: After refmac, R = 0.2252 (Rfree = 0.000) for 12173 atoms. Found 16 (58 requested) and removed 72 (29 requested) atoms. Cycle 5: After refmac, R = 0.2285 (Rfree = 0.000) for 12062 atoms. Found 25 (57 requested) and removed 67 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 4.03 Search for helices and strands: 0 residues in 0 chains, 12482 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 12505 seeds are put forward Round 1: 732 peptides, 145 chains. Longest chain 12 peptides. Score 0.329 Round 2: 828 peptides, 136 chains. Longest chain 17 peptides. Score 0.456 Round 3: 845 peptides, 133 chains. Longest chain 16 peptides. Score 0.482 Round 4: 865 peptides, 126 chains. Longest chain 18 peptides. Score 0.524 Round 5: 885 peptides, 129 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 5 Chains 133, Residues 756, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 27912 restraints for refining 12195 atoms. 24880 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2371 (Rfree = 0.000) for 12195 atoms. Found 34 (57 requested) and removed 115 (28 requested) atoms. Cycle 7: After refmac, R = 0.2319 (Rfree = 0.000) for 11993 atoms. Found 37 (57 requested) and removed 95 (28 requested) atoms. Cycle 8: After refmac, R = 0.1882 (Rfree = 0.000) for 11866 atoms. Found 14 (56 requested) and removed 55 (28 requested) atoms. Cycle 9: After refmac, R = 0.1826 (Rfree = 0.000) for 11785 atoms. Found 9 (56 requested) and removed 50 (28 requested) atoms. Cycle 10: After refmac, R = 0.1750 (Rfree = 0.000) for 11719 atoms. Found 13 (55 requested) and removed 46 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 12154 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 12167 seeds are put forward Round 1: 684 peptides, 135 chains. Longest chain 12 peptides. Score 0.323 Round 2: 805 peptides, 126 chains. Longest chain 23 peptides. Score 0.474 Round 3: 785 peptides, 118 chains. Longest chain 16 peptides. Score 0.487 Round 4: 819 peptides, 127 chains. Longest chain 18 peptides. Score 0.482 Round 5: 835 peptides, 126 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 5 Chains 126, Residues 709, Estimated correctness of the model 0.0 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28828 restraints for refining 12379 atoms. 26004 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2367 (Rfree = 0.000) for 12379 atoms. Found 41 (58 requested) and removed 122 (29 requested) atoms. Cycle 12: After refmac, R = 0.2093 (Rfree = 0.000) for 12185 atoms. Found 41 (58 requested) and removed 108 (29 requested) atoms. Cycle 13: After refmac, R = 0.2089 (Rfree = 0.000) for 12056 atoms. Found 38 (57 requested) and removed 71 (28 requested) atoms. Cycle 14: After refmac, R = 0.1930 (Rfree = 0.000) for 11986 atoms. Found 30 (57 requested) and removed 82 (28 requested) atoms. Cycle 15: After refmac, R = 0.1612 (Rfree = 0.000) for 11912 atoms. Found 13 (56 requested) and removed 42 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 12305 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12324 seeds are put forward Round 1: 663 peptides, 127 chains. Longest chain 15 peptides. Score 0.336 Round 2: 778 peptides, 128 chains. Longest chain 18 peptides. Score 0.442 Round 3: 763 peptides, 115 chains. Longest chain 21 peptides. Score 0.479 Round 4: 733 peptides, 113 chains. Longest chain 24 peptides. Score 0.460 Round 5: 749 peptides, 112 chains. Longest chain 20 peptides. Score 0.478 Taking the results from Round 3 Chains 115, Residues 648, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29114 restraints for refining 12556 atoms. 26549 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1987 (Rfree = 0.000) for 12556 atoms. Found 23 (59 requested) and removed 127 (29 requested) atoms. Cycle 17: After refmac, R = 0.2015 (Rfree = 0.000) for 12370 atoms. Found 36 (59 requested) and removed 89 (29 requested) atoms. Cycle 18: After refmac, R = 0.2005 (Rfree = 0.000) for 12262 atoms. Found 33 (58 requested) and removed 63 (29 requested) atoms. Cycle 19: After refmac, R = 0.1567 (Rfree = 0.000) for 12188 atoms. Found 13 (58 requested) and removed 51 (29 requested) atoms. Cycle 20: After refmac, R = 0.1462 (Rfree = 0.000) for 12096 atoms. Found 10 (57 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 12437 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 12474 seeds are put forward Round 1: 641 peptides, 132 chains. Longest chain 13 peptides. Score 0.292 Round 2: 741 peptides, 127 chains. Longest chain 15 peptides. Score 0.412 Round 3: 754 peptides, 121 chains. Longest chain 17 peptides. Score 0.448 Round 4: 762 peptides, 120 chains. Longest chain 16 peptides. Score 0.459 Round 5: 798 peptides, 119 chains. Longest chain 21 peptides. Score 0.494 Taking the results from Round 5 Chains 121, Residues 679, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28886 restraints for refining 12560 atoms. 26161 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2177 (Rfree = 0.000) for 12560 atoms. Found 38 (59 requested) and removed 146 (29 requested) atoms. Cycle 22: After refmac, R = 0.2036 (Rfree = 0.000) for 12370 atoms. Found 50 (59 requested) and removed 74 (29 requested) atoms. Cycle 23: After refmac, R = 0.1945 (Rfree = 0.000) for 12283 atoms. Found 38 (58 requested) and removed 65 (29 requested) atoms. Cycle 24: After refmac, R = 0.1984 (Rfree = 0.000) for 12210 atoms. Found 37 (58 requested) and removed 61 (29 requested) atoms. Cycle 25: After refmac, R = 0.2001 (Rfree = 0.000) for 12155 atoms. Found 49 (57 requested) and removed 56 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 12492 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 12519 seeds are put forward Round 1: 603 peptides, 125 chains. Longest chain 13 peptides. Score 0.282 Round 2: 696 peptides, 121 chains. Longest chain 14 peptides. Score 0.394 Round 3: 671 peptides, 115 chains. Longest chain 14 peptides. Score 0.395 Round 4: 695 peptides, 118 chains. Longest chain 15 peptides. Score 0.405 Round 5: 701 peptides, 116 chains. Longest chain 20 peptides. Score 0.419 Taking the results from Round 5 Chains 118, Residues 585, Estimated correctness of the model 0.0 % 7 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29559 restraints for refining 12617 atoms. 27254 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2250 (Rfree = 0.000) for 12617 atoms. Found 53 (59 requested) and removed 166 (29 requested) atoms. Cycle 27: After refmac, R = 0.2133 (Rfree = 0.000) for 12445 atoms. Found 53 (59 requested) and removed 82 (29 requested) atoms. Cycle 28: After refmac, R = 0.2109 (Rfree = 0.000) for 12360 atoms. Found 58 (58 requested) and removed 78 (29 requested) atoms. Cycle 29: After refmac, R = 0.1987 (Rfree = 0.000) for 12298 atoms. Found 58 (58 requested) and removed 63 (29 requested) atoms. Cycle 30: After refmac, R = 0.1621 (Rfree = 0.000) for 12257 atoms. Found 16 (58 requested) and removed 47 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 12597 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 12610 seeds are put forward Round 1: 523 peptides, 113 chains. Longest chain 9 peptides. Score 0.250 Round 2: 610 peptides, 117 chains. Longest chain 12 peptides. Score 0.325 Round 3: 625 peptides, 112 chains. Longest chain 13 peptides. Score 0.362 Round 4: 649 peptides, 113 chains. Longest chain 21 peptides. Score 0.382 Round 5: 624 peptides, 109 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 4 Chains 114, Residues 536, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29320 restraints for refining 12568 atoms. 27204 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2079 (Rfree = 0.000) for 12568 atoms. Found 59 (59 requested) and removed 111 (29 requested) atoms. Cycle 32: After refmac, R = 0.2024 (Rfree = 0.000) for 12443 atoms. Found 59 (59 requested) and removed 87 (29 requested) atoms. Cycle 33: After refmac, R = 0.1611 (Rfree = 0.000) for 12378 atoms. Found 11 (58 requested) and removed 58 (29 requested) atoms. Cycle 34: After refmac, R = 0.1435 (Rfree = 0.000) for 12314 atoms. Found 10 (58 requested) and removed 43 (29 requested) atoms. Cycle 35: After refmac, R = 0.1451 (Rfree = 0.000) for 12267 atoms. Found 15 (58 requested) and removed 40 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 12569 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 12602 seeds are put forward Round 1: 523 peptides, 109 chains. Longest chain 11 peptides. Score 0.268 Round 2: 618 peptides, 120 chains. Longest chain 11 peptides. Score 0.320 Round 3: 629 peptides, 115 chains. Longest chain 11 peptides. Score 0.353 Round 4: 615 peptides, 110 chains. Longest chain 15 peptides. Score 0.361 Round 5: 622 peptides, 108 chains. Longest chain 14 peptides. Score 0.376 Taking the results from Round 5 Chains 108, Residues 514, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 29521 restraints for refining 12561 atoms. 27544 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2035 (Rfree = 0.000) for 12561 atoms. Found 54 (59 requested) and removed 120 (29 requested) atoms. Cycle 37: After refmac, R = 0.1978 (Rfree = 0.000) for 12453 atoms. Found 59 (59 requested) and removed 63 (29 requested) atoms. Cycle 38: After refmac, R = 0.2038 (Rfree = 0.000) for 12419 atoms. Found 59 (59 requested) and removed 70 (29 requested) atoms. Cycle 39: After refmac, R = 0.1993 (Rfree = 0.000) for 12360 atoms. Found 58 (58 requested) and removed 54 (29 requested) atoms. Cycle 40: After refmac, R = 0.2059 (Rfree = 0.000) for 12328 atoms. Found 58 (58 requested) and removed 51 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 4.01 Search for helices and strands: 0 residues in 0 chains, 12625 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 12640 seeds are put forward Round 1: 439 peptides, 101 chains. Longest chain 10 peptides. Score 0.210 Round 2: 501 peptides, 93 chains. Longest chain 11 peptides. Score 0.319 Round 3: 467 peptides, 86 chains. Longest chain 16 peptides. Score 0.315 Round 4: 463 peptides, 85 chains. Longest chain 15 peptides. Score 0.315 Round 5: 471 peptides, 85 chains. Longest chain 18 peptides. Score 0.324 Taking the results from Round 5 Chains 85, Residues 386, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 14774 reflections ( 99.96 % complete ) and 28795 restraints for refining 12221 atoms. 27262 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2091 (Rfree = 0.000) for 12221 atoms. Found 58 (58 requested) and removed 91 (29 requested) atoms. Cycle 42: After refmac, R = 0.2079 (Rfree = 0.000) for 12137 atoms. Found 57 (57 requested) and removed 64 (28 requested) atoms. Cycle 43: After refmac, R = 0.2128 (Rfree = 0.000) for 12093 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. Cycle 44: After refmac, R = 0.2060 (Rfree = 0.000) for 12055 atoms. Found 57 (57 requested) and removed 44 (28 requested) atoms. Cycle 45: After refmac, R = 0.2073 (Rfree = 0.000) for 12038 atoms. Found 57 (57 requested) and removed 58 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 12347 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12366 seeds are put forward Round 1: 350 peptides, 80 chains. Longest chain 8 peptides. Score 0.207 Round 2: 441 peptides, 90 chains. Longest chain 12 peptides. Score 0.266 Round 3: 436 peptides, 85 chains. Longest chain 10 peptides. Score 0.285 Round 4: 392 peptides, 74 chains. Longest chain 12 peptides. Score 0.289 Round 5: 396 peptides, 76 chains. Longest chain 11 peptides. Score 0.283 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 318, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkm-4_warpNtrace.pdb as input Building loops using Loopy2018 74 chains (318 residues) following loop building 3 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14774 reflections ( 99.96 % complete ) and 26858 restraints for refining 11440 atoms. 25642 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2177 (Rfree = 0.000) for 11440 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2116 (Rfree = 0.000) for 11377 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1987 (Rfree = 0.000) for 11328 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2020 (Rfree = 0.000) for 11289 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:54:07 GMT 2018 Job finished. TimeTaking 108.04 Used memory is bytes: 19482648