Mon 24 Dec 07:32:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vme-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-noncs ############### 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 07:32:59 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/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-noncs/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 642 and 0 Target number of residues in the AU: 642 Target solvent content: 0.6343 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-3.2-parrot-noncs.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: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.70 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: 48.998 3.200 Wilson plot Bfac: 68.69 15542 reflections ( 99.87 % complete ) and 0 restraints for refining 7316 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3130 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 7316 atoms. Found 65 (65 requested) and removed 83 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 7461 seeds are put forward NCS extension: 0 residues added, 7461 seeds are put forward Round 1: 448 peptides, 81 chains. Longest chain 12 peptides. Score 0.395 Round 2: 510 peptides, 65 chains. Longest chain 17 peptides. Score 0.590 Round 3: 509 peptides, 65 chains. Longest chain 18 peptides. Score 0.589 Round 4: 558 peptides, 58 chains. Longest chain 34 peptides. Score 0.683 Round 5: 580 peptides, 61 chains. Longest chain 36 peptides. Score 0.691 Taking the results from Round 5 Chains 65, Residues 519, Estimated correctness of the model 63.2 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12308 restraints for refining 5987 atoms. 10047 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2668 (Rfree = 0.000) for 5987 atoms. Found 50 (53 requested) and removed 55 (26 requested) atoms. Cycle 2: After refmac, R = 0.2532 (Rfree = 0.000) for 5934 atoms. Found 17 (53 requested) and removed 43 (26 requested) atoms. Cycle 3: After refmac, R = 0.2528 (Rfree = 0.000) for 5895 atoms. Found 17 (53 requested) and removed 33 (26 requested) atoms. Cycle 4: After refmac, R = 0.2452 (Rfree = 0.000) for 5871 atoms. Found 14 (52 requested) and removed 37 (26 requested) atoms. Cycle 5: After refmac, R = 0.2582 (Rfree = 0.000) for 5840 atoms. Found 33 (52 requested) and removed 35 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6009 seeds are put forward NCS extension: 8 residues added (6 deleted due to clashes), 6017 seeds are put forward Round 1: 520 peptides, 72 chains. Longest chain 22 peptides. Score 0.562 Round 2: 581 peptides, 65 chains. Longest chain 35 peptides. Score 0.673 Round 3: 582 peptides, 57 chains. Longest chain 32 peptides. Score 0.711 Round 4: 569 peptides, 57 chains. Longest chain 40 peptides. Score 0.698 Round 5: 582 peptides, 61 chains. Longest chain 29 peptides. Score 0.693 Taking the results from Round 3 Chains 62, Residues 525, Estimated correctness of the model 67.5 % 7 chains (86 residues) have been docked in sequence Building loops using Loopy2018 62 chains (525 residues) following loop building 7 chains (86 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12180 restraints for refining 5988 atoms. 9839 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2677 (Rfree = 0.000) for 5988 atoms. Found 32 (53 requested) and removed 48 (26 requested) atoms. Cycle 7: After refmac, R = 0.2537 (Rfree = 0.000) for 5949 atoms. Found 16 (52 requested) and removed 29 (26 requested) atoms. Cycle 8: After refmac, R = 0.2484 (Rfree = 0.000) for 5923 atoms. Found 24 (51 requested) and removed 32 (26 requested) atoms. Cycle 9: After refmac, R = 0.2435 (Rfree = 0.000) for 5889 atoms. Found 22 (50 requested) and removed 38 (26 requested) atoms. Cycle 10: After refmac, R = 0.2456 (Rfree = 0.000) for 5863 atoms. Found 16 (48 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 6060 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6085 seeds are put forward Round 1: 517 peptides, 70 chains. Longest chain 29 peptides. Score 0.570 Round 2: 561 peptides, 61 chains. Longest chain 39 peptides. Score 0.671 Round 3: 566 peptides, 60 chains. Longest chain 28 peptides. Score 0.681 Round 4: 573 peptides, 54 chains. Longest chain 34 peptides. Score 0.716 Round 5: 549 peptides, 57 chains. Longest chain 41 peptides. Score 0.678 Taking the results from Round 4 Chains 59, Residues 519, Estimated correctness of the model 68.5 % 7 chains (115 residues) have been docked in sequence Building loops using Loopy2018 59 chains (519 residues) following loop building 7 chains (115 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11683 restraints for refining 5987 atoms. 9179 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2607 (Rfree = 0.000) for 5987 atoms. Found 35 (48 requested) and removed 51 (26 requested) atoms. Cycle 12: After refmac, R = 0.2579 (Rfree = 0.000) for 5956 atoms. Found 47 (47 requested) and removed 37 (26 requested) atoms. Cycle 13: After refmac, R = 0.2590 (Rfree = 0.000) for 5942 atoms. Found 46 (46 requested) and removed 40 (26 requested) atoms. Cycle 14: After refmac, R = 0.2325 (Rfree = 0.000) for 5939 atoms. Found 13 (45 requested) and removed 33 (26 requested) atoms. Cycle 15: After refmac, R = 0.2283 (Rfree = 0.000) for 5911 atoms. Found 28 (43 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6092 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 6116 seeds are put forward Round 1: 514 peptides, 73 chains. Longest chain 16 peptides. Score 0.548 Round 2: 558 peptides, 64 chains. Longest chain 27 peptides. Score 0.653 Round 3: 556 peptides, 60 chains. Longest chain 31 peptides. Score 0.671 Round 4: 572 peptides, 60 chains. Longest chain 31 peptides. Score 0.687 Round 5: 557 peptides, 57 chains. Longest chain 30 peptides. Score 0.686 Taking the results from Round 4 Chains 60, Residues 512, Estimated correctness of the model 62.4 % 6 chains (106 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11916 restraints for refining 5989 atoms. 9503 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2451 (Rfree = 0.000) for 5989 atoms. Found 37 (42 requested) and removed 34 (26 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2295 (Rfree = 0.000) for 5974 atoms. Found 23 (42 requested) and removed 29 (26 requested) atoms. Cycle 18: After refmac, R = 0.2234 (Rfree = 0.000) for 5958 atoms. Found 10 (42 requested) and removed 28 (26 requested) atoms. Cycle 19: After refmac, R = 0.2382 (Rfree = 0.000) for 5928 atoms. Found 38 (42 requested) and removed 30 (26 requested) atoms. Cycle 20: After refmac, R = 0.2203 (Rfree = 0.000) for 5925 atoms. Found 20 (42 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6082 seeds are put forward NCS extension: 16 residues added (18 deleted due to clashes), 6098 seeds are put forward Round 1: 498 peptides, 68 chains. Longest chain 30 peptides. Score 0.556 Round 2: 549 peptides, 61 chains. Longest chain 26 peptides. Score 0.658 Round 3: 543 peptides, 62 chains. Longest chain 39 peptides. Score 0.646 Round 4: 563 peptides, 65 chains. Longest chain 19 peptides. Score 0.653 Round 5: 559 peptides, 64 chains. Longest chain 44 peptides. Score 0.654 Taking the results from Round 2 Chains 65, Residues 488, Estimated correctness of the model 55.7 % 8 chains (82 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12371 restraints for refining 5989 atoms. 10171 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2304 (Rfree = 0.000) for 5989 atoms. Found 21 (42 requested) and removed 35 (26 requested) atoms. Cycle 22: After refmac, R = 0.2194 (Rfree = 0.000) for 5965 atoms. Found 10 (42 requested) and removed 26 (26 requested) atoms. Cycle 23: After refmac, R = 0.2092 (Rfree = 0.000) for 5942 atoms. Found 12 (42 requested) and removed 26 (26 requested) atoms. Cycle 24: After refmac, R = 0.2057 (Rfree = 0.000) for 5918 atoms. Found 14 (42 requested) and removed 26 (26 requested) atoms. Cycle 25: After refmac, R = 0.2050 (Rfree = 0.000) for 5898 atoms. Found 12 (42 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6020 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6043 seeds are put forward Round 1: 504 peptides, 68 chains. Longest chain 30 peptides. Score 0.564 Round 2: 556 peptides, 62 chains. Longest chain 39 peptides. Score 0.661 Round 3: 567 peptides, 70 chains. Longest chain 27 peptides. Score 0.632 Round 4: 584 peptides, 58 chains. Longest chain 54 peptides. Score 0.708 Round 5: 551 peptides, 57 chains. Longest chain 34 peptides. Score 0.680 Taking the results from Round 4 Chains 61, Residues 526, Estimated correctness of the model 66.9 % 7 chains (131 residues) have been docked in sequence Building loops using Loopy2018 61 chains (526 residues) following loop building 7 chains (131 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11409 restraints for refining 5989 atoms. 8835 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2497 (Rfree = 0.000) for 5989 atoms. Found 36 (42 requested) and removed 49 (26 requested) atoms. Cycle 27: After refmac, R = 0.2258 (Rfree = 0.000) for 5957 atoms. Found 16 (41 requested) and removed 31 (26 requested) atoms. Cycle 28: After refmac, R = 0.2211 (Rfree = 0.000) for 5934 atoms. Found 12 (40 requested) and removed 27 (26 requested) atoms. Cycle 29: After refmac, R = 0.2125 (Rfree = 0.000) for 5906 atoms. Found 16 (39 requested) and removed 27 (26 requested) atoms. Cycle 30: After refmac, R = 0.2062 (Rfree = 0.000) for 5884 atoms. Found 4 (37 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6053 seeds are put forward NCS extension: 23 residues added (8 deleted due to clashes), 6076 seeds are put forward Round 1: 516 peptides, 67 chains. Longest chain 31 peptides. Score 0.586 Round 2: 540 peptides, 56 chains. Longest chain 49 peptides. Score 0.673 Round 3: 544 peptides, 59 chains. Longest chain 25 peptides. Score 0.663 Round 4: 539 peptides, 61 chains. Longest chain 28 peptides. Score 0.647 Round 5: 561 peptides, 50 chains. Longest chain 49 peptides. Score 0.723 Taking the results from Round 5 Chains 50, Residues 511, Estimated correctness of the model 69.9 % 5 chains (97 residues) have been docked in sequence Building loops using Loopy2018 50 chains (511 residues) following loop building 5 chains (97 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11969 restraints for refining 5989 atoms. 9595 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2362 (Rfree = 0.000) for 5989 atoms. Found 32 (37 requested) and removed 42 (26 requested) atoms. Cycle 32: After refmac, R = 0.2191 (Rfree = 0.000) for 5966 atoms. Found 21 (36 requested) and removed 28 (26 requested) atoms. Cycle 33: After refmac, R = 0.2249 (Rfree = 0.000) for 5946 atoms. Found 26 (35 requested) and removed 28 (26 requested) atoms. Cycle 34: After refmac, R = 0.2115 (Rfree = 0.000) for 5940 atoms. Found 10 (34 requested) and removed 28 (26 requested) atoms. Cycle 35: After refmac, R = 0.2256 (Rfree = 0.000) for 5917 atoms. Found 33 (33 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6106 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 6133 seeds are put forward Round 1: 469 peptides, 71 chains. Longest chain 28 peptides. Score 0.496 Round 2: 506 peptides, 54 chains. Longest chain 40 peptides. Score 0.646 Round 3: 504 peptides, 57 chains. Longest chain 26 peptides. Score 0.627 Round 4: 516 peptides, 59 chains. Longest chain 27 peptides. Score 0.631 Round 5: 538 peptides, 60 chains. Longest chain 49 peptides. Score 0.651 Taking the results from Round 5 Chains 63, Residues 478, Estimated correctness of the model 54.1 % 10 chains (157 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11479 restraints for refining 5989 atoms. 9025 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2466 (Rfree = 0.000) for 5989 atoms. Found 32 (32 requested) and removed 45 (26 requested) atoms. Cycle 37: After refmac, R = 0.2250 (Rfree = 0.000) for 5960 atoms. Found 16 (32 requested) and removed 37 (26 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 5926 atoms. Found 13 (32 requested) and removed 29 (26 requested) atoms. Cycle 39: After refmac, R = 0.2378 (Rfree = 0.000) for 5904 atoms. Found 32 (32 requested) and removed 27 (26 requested) atoms. Cycle 40: After refmac, R = 0.2126 (Rfree = 0.000) for 5905 atoms. Found 18 (32 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 6057 seeds are put forward NCS extension: 23 residues added (11 deleted due to clashes), 6080 seeds are put forward Round 1: 437 peptides, 65 chains. Longest chain 25 peptides. Score 0.488 Round 2: 482 peptides, 61 chains. Longest chain 39 peptides. Score 0.577 Round 3: 500 peptides, 62 chains. Longest chain 33 peptides. Score 0.594 Round 4: 503 peptides, 59 chains. Longest chain 28 peptides. Score 0.615 Round 5: 507 peptides, 62 chains. Longest chain 24 peptides. Score 0.603 Taking the results from Round 4 Chains 62, Residues 444, Estimated correctness of the model 45.0 % 6 chains (78 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12427 restraints for refining 5989 atoms. 10386 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2245 (Rfree = 0.000) for 5989 atoms. Found 27 (32 requested) and removed 33 (26 requested) atoms. Cycle 42: After refmac, R = 0.2346 (Rfree = 0.000) for 5975 atoms. Found 32 (32 requested) and removed 35 (26 requested) atoms. Cycle 43: After refmac, R = 0.2062 (Rfree = 0.000) for 5960 atoms. Found 13 (32 requested) and removed 28 (26 requested) atoms. Cycle 44: After refmac, R = 0.2128 (Rfree = 0.000) for 5935 atoms. Found 22 (32 requested) and removed 30 (26 requested) atoms. Cycle 45: After refmac, R = 0.2002 (Rfree = 0.000) for 5924 atoms. Found 8 (32 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 6073 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 6085 seeds are put forward Round 1: 435 peptides, 66 chains. Longest chain 22 peptides. Score 0.478 Round 2: 472 peptides, 63 chains. Longest chain 23 peptides. Score 0.551 Round 3: 483 peptides, 63 chains. Longest chain 23 peptides. Score 0.566 Round 4: 496 peptides, 59 chains. Longest chain 22 peptides. Score 0.606 Round 5: 508 peptides, 66 chains. Longest chain 19 peptides. Score 0.581 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 437, Estimated correctness of the model 42.7 % 6 chains (71 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 62 chains (437 residues) following loop building 6 chains (71 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15542 reflections ( 99.87 % complete ) and 12538 restraints for refining 5989 atoms. 10560 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2202 (Rfree = 0.000) for 5989 atoms. Found 0 (32 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2452 (Rfree = 0.000) for 5954 atoms. Found 0 (32 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2116 (Rfree = 0.000) for 5917 atoms. Found 0 (32 requested) and removed 26 (26 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2431 (Rfree = 0.000) for 5887 atoms. TimeTaking 66.65