Sun 23 Dec 23:57:54 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 1vm8-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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/1vm8-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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 ============================================================ Sun 23 Dec 23:57:59 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/1vm8-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-2.5-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 1004 and 0 Target number of residues in the AU: 1004 Target solvent content: 0.5622 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-2.5-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: 4 Cell parameters: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.50 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: 105.560 2.500 Wilson plot Bfac: 39.13 42288 reflections ( 99.19 % complete ) and 0 restraints for refining 9415 atoms. Observations/parameters ratio is 1.12 ------------------------------------------------------ Starting model: R = 0.3417 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2569 (Rfree = 0.000) for 9415 atoms. Found 119 (170 requested) and removed 176 (85 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.57 2.47 NCS extension: 0 residues added, 9358 seeds are put forward Round 1: 501 peptides, 96 chains. Longest chain 11 peptides. Score 0.339 Round 2: 561 peptides, 88 chains. Longest chain 24 peptides. Score 0.460 Round 3: 585 peptides, 91 chains. Longest chain 20 peptides. Score 0.473 Round 4: 603 peptides, 85 chains. Longest chain 27 peptides. Score 0.524 Round 5: 613 peptides, 80 chains. Longest chain 27 peptides. Score 0.558 Taking the results from Round 5 Chains 87, Residues 533, Estimated correctness of the model 67.6 % 12 chains (148 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 16268 restraints for refining 8004 atoms. 13720 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2847 (Rfree = 0.000) for 8004 atoms. Found 134 (145 requested) and removed 93 (72 requested) atoms. Cycle 2: After refmac, R = 0.2676 (Rfree = 0.000) for 7988 atoms. Found 72 (145 requested) and removed 79 (72 requested) atoms. Cycle 3: After refmac, R = 0.2623 (Rfree = 0.000) for 7951 atoms. Found 70 (144 requested) and removed 78 (72 requested) atoms. Cycle 4: After refmac, R = 0.2559 (Rfree = 0.000) for 7930 atoms. Found 83 (144 requested) and removed 73 (72 requested) atoms. Cycle 5: After refmac, R = 0.2517 (Rfree = 0.000) for 7924 atoms. Found 85 (144 requested) and removed 72 (72 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.58 2.48 NCS extension: 3 residues added (2 deleted due to clashes), 7972 seeds are put forward Round 1: 599 peptides, 81 chains. Longest chain 34 peptides. Score 0.539 Round 2: 638 peptides, 73 chains. Longest chain 37 peptides. Score 0.615 Round 3: 659 peptides, 75 chains. Longest chain 39 peptides. Score 0.626 Round 4: 668 peptides, 73 chains. Longest chain 34 peptides. Score 0.642 Round 5: 685 peptides, 77 chains. Longest chain 39 peptides. Score 0.641 Taking the results from Round 4 Chains 74, Residues 595, Estimated correctness of the model 78.0 % 15 chains (223 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 14801 restraints for refining 8006 atoms. 11656 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2620 (Rfree = 0.000) for 8006 atoms. Found 115 (145 requested) and removed 85 (72 requested) atoms. Cycle 7: After refmac, R = 0.2460 (Rfree = 0.000) for 8001 atoms. Found 84 (145 requested) and removed 74 (72 requested) atoms. Cycle 8: After refmac, R = 0.2402 (Rfree = 0.000) for 7995 atoms. Found 76 (145 requested) and removed 72 (72 requested) atoms. Cycle 9: After refmac, R = 0.2374 (Rfree = 0.000) for 7986 atoms. Found 71 (145 requested) and removed 73 (72 requested) atoms. Cycle 10: After refmac, R = 0.2343 (Rfree = 0.000) for 7968 atoms. Found 62 (144 requested) and removed 77 (72 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.56 2.46 NCS extension: 36 residues added (22 deleted due to clashes), 8010 seeds are put forward Round 1: 639 peptides, 77 chains. Longest chain 32 peptides. Score 0.598 Round 2: 669 peptides, 68 chains. Longest chain 59 peptides. Score 0.663 Round 3: 678 peptides, 68 chains. Longest chain 38 peptides. Score 0.671 Round 4: 688 peptides, 70 chains. Longest chain 41 peptides. Score 0.671 Round 5: 677 peptides, 68 chains. Longest chain 46 peptides. Score 0.670 Taking the results from Round 4 Chains 77, Residues 618, Estimated correctness of the model 81.1 % 18 chains (291 residues) have been docked in sequence ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13730 restraints for refining 8006 atoms. 10200 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2497 (Rfree = 0.000) for 8006 atoms. Found 119 (145 requested) and removed 87 (72 requested) atoms. Cycle 12: After refmac, R = 0.2339 (Rfree = 0.000) for 8011 atoms. Found 80 (145 requested) and removed 73 (72 requested) atoms. Cycle 13: After refmac, R = 0.2305 (Rfree = 0.000) for 8002 atoms. Found 55 (145 requested) and removed 74 (72 requested) atoms. Cycle 14: After refmac, R = 0.2316 (Rfree = 0.000) for 7971 atoms. Found 84 (144 requested) and removed 72 (72 requested) atoms. Cycle 15: After refmac, R = 0.2275 (Rfree = 0.000) for 7974 atoms. Found 65 (144 requested) and removed 75 (72 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.56 2.46 NCS extension: 82 residues added (38 deleted due to clashes), 8077 seeds are put forward Round 1: 625 peptides, 72 chains. Longest chain 31 peptides. Score 0.607 Round 2: 674 peptides, 60 chains. Longest chain 39 peptides. Score 0.698 Round 3: 670 peptides, 62 chains. Longest chain 57 peptides. Score 0.688 Round 4: 683 peptides, 60 chains. Longest chain 60 peptides. Score 0.705 Round 5: 677 peptides, 62 chains. Longest chain 51 peptides. Score 0.693 Taking the results from Round 4 Chains 65, Residues 623, Estimated correctness of the model 84.5 % 18 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 272 A and 280 A 62 chains (626 residues) following loop building 17 chains (365 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 12923 restraints for refining 8006 atoms. 9050 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 8006 atoms. Found 108 (145 requested) and removed 84 (72 requested) atoms. Cycle 17: After refmac, R = 0.2331 (Rfree = 0.000) for 8013 atoms. Found 74 (142 requested) and removed 73 (72 requested) atoms. Cycle 18: After refmac, R = 0.2267 (Rfree = 0.000) for 7996 atoms. Found 68 (139 requested) and removed 75 (72 requested) atoms. Cycle 19: After refmac, R = 0.2229 (Rfree = 0.000) for 7979 atoms. Found 69 (135 requested) and removed 74 (72 requested) atoms. Cycle 20: After refmac, R = 0.2214 (Rfree = 0.000) for 7962 atoms. Found 67 (132 requested) and removed 73 (72 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.55 2.45 NCS extension: 457 residues added (102 deleted due to clashes), 8433 seeds are put forward Round 1: 632 peptides, 69 chains. Longest chain 58 peptides. Score 0.627 Round 2: 663 peptides, 66 chains. Longest chain 59 peptides. Score 0.666 Round 3: 686 peptides, 61 chains. Longest chain 65 peptides. Score 0.704 Round 4: 677 peptides, 62 chains. Longest chain 60 peptides. Score 0.693 Round 5: 670 peptides, 67 chains. Longest chain 58 peptides. Score 0.668 Taking the results from Round 3 Chains 72, Residues 625, Estimated correctness of the model 84.4 % 14 chains (283 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 272 A and 275 A Built loop between residues 305 B and 311 B 69 chains (629 residues) following loop building 12 chains (290 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13680 restraints for refining 8005 atoms. 10076 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2378 (Rfree = 0.000) for 8005 atoms. Found 124 (130 requested) and removed 79 (72 requested) atoms. Cycle 22: After refmac, R = 0.2207 (Rfree = 0.000) for 8043 atoms. Found 76 (128 requested) and removed 73 (73 requested) atoms. Cycle 23: After refmac, R = 0.2178 (Rfree = 0.000) for 8038 atoms. Found 71 (125 requested) and removed 73 (72 requested) atoms. Cycle 24: After refmac, R = 0.2157 (Rfree = 0.000) for 8032 atoms. Found 74 (122 requested) and removed 74 (72 requested) atoms. Cycle 25: After refmac, R = 0.2174 (Rfree = 0.000) for 8023 atoms. Found 75 (119 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.55 2.45 NCS extension: 142 residues added (45 deleted due to clashes), 8198 seeds are put forward Round 1: 660 peptides, 68 chains. Longest chain 38 peptides. Score 0.656 Round 2: 686 peptides, 61 chains. Longest chain 60 peptides. Score 0.704 Round 3: 693 peptides, 54 chains. Longest chain 80 peptides. Score 0.734 Round 4: 689 peptides, 59 chains. Longest chain 58 peptides. Score 0.713 Round 5: 675 peptides, 61 chains. Longest chain 57 peptides. Score 0.695 Taking the results from Round 3 Chains 61, Residues 639, Estimated correctness of the model 87.2 % 15 chains (366 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 275 A and 285 A Built loop between residues 178 B and 189 B Built loop between residues 271 B and 281 B Built loop between residues 447 B and 452 B 55 chains (660 residues) following loop building 11 chains (398 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 12121 restraints for refining 8006 atoms. 7967 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2486 (Rfree = 0.000) for 8006 atoms. Found 116 (116 requested) and removed 87 (72 requested) atoms. Cycle 27: After refmac, R = 0.2350 (Rfree = 0.000) for 8015 atoms. Found 96 (113 requested) and removed 72 (72 requested) atoms. Cycle 28: After refmac, R = 0.2293 (Rfree = 0.000) for 8021 atoms. Found 78 (110 requested) and removed 73 (72 requested) atoms. Cycle 29: After refmac, R = 0.2274 (Rfree = 0.000) for 8019 atoms. Found 65 (107 requested) and removed 73 (72 requested) atoms. Cycle 30: After refmac, R = 0.2247 (Rfree = 0.000) for 8003 atoms. Found 86 (104 requested) and removed 73 (72 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.55 2.45 NCS extension: 271 residues added (38 deleted due to clashes), 8324 seeds are put forward Round 1: 661 peptides, 63 chains. Longest chain 51 peptides. Score 0.676 Round 2: 695 peptides, 59 chains. Longest chain 55 peptides. Score 0.718 Round 3: 688 peptides, 58 chains. Longest chain 88 peptides. Score 0.716 Round 4: 673 peptides, 61 chains. Longest chain 50 peptides. Score 0.694 Round 5: 667 peptides, 61 chains. Longest chain 51 peptides. Score 0.689 Taking the results from Round 2 Chains 65, Residues 636, Estimated correctness of the model 85.8 % 13 chains (317 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 61 A 63 chains (639 residues) following loop building 12 chains (321 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13133 restraints for refining 8005 atoms. 9326 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2373 (Rfree = 0.000) for 8005 atoms. Found 101 (101 requested) and removed 84 (72 requested) atoms. Cycle 32: After refmac, R = 0.2241 (Rfree = 0.000) for 8010 atoms. Found 79 (99 requested) and removed 73 (72 requested) atoms. Cycle 33: After refmac, R = 0.2248 (Rfree = 0.000) for 8003 atoms. Found 74 (96 requested) and removed 73 (72 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 7993 atoms. Found 69 (93 requested) and removed 73 (72 requested) atoms. Cycle 35: After refmac, R = 0.2222 (Rfree = 0.000) for 7976 atoms. Found 81 (89 requested) and removed 72 (72 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.56 2.46 NCS extension: 53 residues added (51 deleted due to clashes), 8059 seeds are put forward Round 1: 656 peptides, 62 chains. Longest chain 43 peptides. Score 0.676 Round 2: 671 peptides, 54 chains. Longest chain 68 peptides. Score 0.718 Round 3: 690 peptides, 57 chains. Longest chain 62 peptides. Score 0.721 Round 4: 674 peptides, 59 chains. Longest chain 58 peptides. Score 0.702 Round 5: 676 peptides, 56 chains. Longest chain 51 peptides. Score 0.715 Taking the results from Round 3 Chains 60, Residues 633, Estimated correctness of the model 86.0 % 12 chains (306 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 273 A and 280 A 58 chains (636 residues) following loop building 11 chains (312 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 13229 restraints for refining 8006 atoms. 9470 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2349 (Rfree = 0.000) for 8006 atoms. Found 87 (87 requested) and removed 84 (72 requested) atoms. Cycle 37: After refmac, R = 0.2267 (Rfree = 0.000) for 7992 atoms. Found 84 (84 requested) and removed 76 (72 requested) atoms. Cycle 38: After refmac, R = 0.2253 (Rfree = 0.000) for 7989 atoms. Found 81 (81 requested) and removed 74 (72 requested) atoms. Cycle 39: After refmac, R = 0.2232 (Rfree = 0.000) for 7988 atoms. Found 78 (78 requested) and removed 75 (72 requested) atoms. Cycle 40: After refmac, R = 0.2223 (Rfree = 0.000) for 7981 atoms. Found 75 (75 requested) and removed 75 (72 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.55 2.45 NCS extension: 268 residues added (106 deleted due to clashes), 8278 seeds are put forward Round 1: 633 peptides, 55 chains. Longest chain 47 peptides. Score 0.685 Round 2: 660 peptides, 45 chains. Longest chain 80 peptides. Score 0.742 Round 3: 660 peptides, 49 chains. Longest chain 111 peptides. Score 0.728 Round 4: 640 peptides, 58 chains. Longest chain 59 peptides. Score 0.679 Round 5: 653 peptides, 52 chains. Longest chain 41 peptides. Score 0.712 Taking the results from Round 2 Chains 50, Residues 615, Estimated correctness of the model 87.9 % 14 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 264 A and 267 A Built loop between residues 277 A and 280 A Built loop between residues 318 A and 325 A Built loop between residues 421 A and 430 A Built loop between residues 308 B and 317 B 43 chains (631 residues) following loop building 9 chains (387 residues) in sequence following loop building ------------------------------------------------------ 42288 reflections ( 99.19 % complete ) and 12591 restraints for refining 8005 atoms. 8594 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2435 (Rfree = 0.000) for 8005 atoms. Found 72 (72 requested) and removed 84 (72 requested) atoms. Cycle 42: After refmac, R = 0.2299 (Rfree = 0.000) for 7980 atoms. Found 72 (72 requested) and removed 74 (72 requested) atoms. Cycle 43: After refmac, R = 0.2301 (Rfree = 0.000) for 7959 atoms. Found 72 (72 requested) and removed 72 (72 requested) atoms. Cycle 44: After refmac, R = 0.2257 (Rfree = 0.000) for 7953 atoms. Found 72 (72 requested) and removed 75 (72 requested) atoms. Cycle 45: After refmac, R = 0.2125 (Rfree = 0.000) for 7942 atoms. Found 66 (72 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.55 2.45 NCS extension: 113 residues added (107 deleted due to clashes), 8071 seeds are put forward Round 1: 630 peptides, 58 chains. Longest chain 42 peptides. Score 0.670 Round 2: 651 peptides, 45 chains. Longest chain 85 peptides. Score 0.736 Round 3: 659 peptides, 55 chains. Longest chain 51 peptides. Score 0.705 Round 4: 684 peptides, 53 chains. Longest chain 74 peptides. Score 0.731 Round 5: 677 peptides, 55 chains. Longest chain 74 peptides. Score 0.719 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 606, Estimated correctness of the model 87.4 % 14 chains (391 residues) have been docked in sequence Sequence coverage is 64 % Consider running further cycles of model building using 1vm8-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 58 A and 63 A Built loop between residues 320 A and 324 A Built loop between residues 336 A and 340 A Built loop between residues 421 A and 429 A 43 chains (622 residues) following loop building 10 chains (408 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 42288 reflections ( 99.19 % complete ) and 12495 restraints for refining 8005 atoms. 8381 conditional restraints added. Observations/parameters ratio is 1.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2372 (Rfree = 0.000) for 8005 atoms. Found 0 (72 requested) and removed 35 (72 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2332 (Rfree = 0.000) for 7955 atoms. Found 0 (72 requested) and removed 11 (72 requested) atoms. Cycle 48: After refmac, R = 0.2309 (Rfree = 0.000) for 7939 atoms. Found 0 (72 requested) and removed 18 (72 requested) atoms. Cycle 49: After refmac, R = 0.2245 (Rfree = 0.000) for 7919 atoms. TimeTaking 104.93