null Mon 24 Dec 07:54:54 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 2gvh-2.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2gvh-2.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2gvh-2.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-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/2gvh-2.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-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 07:54:58 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/2gvh-2.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-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 856 and 0 Target number of residues in the AU: 856 Target solvent content: 0.6147 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-2.6-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-2.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.80 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: 121.211 2.600 Wilson plot Bfac: 58.86 32893 reflections ( 89.68 % complete ) and 0 restraints for refining 7735 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Starting model: R = 0.3677 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2920 (Rfree = 0.000) for 7735 atoms. Found 92 (125 requested) and removed 131 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.85 2.46 NCS extension: 0 residues added, 7696 seeds are put forward Round 1: 432 peptides, 76 chains. Longest chain 13 peptides. Score 0.366 Round 2: 474 peptides, 74 chains. Longest chain 15 peptides. Score 0.435 Round 3: 491 peptides, 70 chains. Longest chain 21 peptides. Score 0.479 Round 4: 526 peptides, 71 chains. Longest chain 22 peptides. Score 0.515 Round 5: 504 peptides, 64 chains. Longest chain 24 peptides. Score 0.526 Taking the results from Round 5 Chains 72, Residues 440, Estimated correctness of the model 58.3 % 12 chains (75 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 13432 restraints for refining 6442 atoms. 11517 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3191 (Rfree = 0.000) for 6442 atoms. Found 103 (104 requested) and removed 87 (52 requested) atoms. Cycle 2: After refmac, R = 0.3129 (Rfree = 0.000) for 6393 atoms. Found 89 (104 requested) and removed 72 (52 requested) atoms. Cycle 3: After refmac, R = 0.3032 (Rfree = 0.000) for 6369 atoms. Found 71 (103 requested) and removed 76 (51 requested) atoms. Cycle 4: After refmac, R = 0.2980 (Rfree = 0.000) for 6341 atoms. Found 83 (103 requested) and removed 70 (51 requested) atoms. Cycle 5: After refmac, R = 0.2904 (Rfree = 0.000) for 6339 atoms. Found 84 (103 requested) and removed 69 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.89 2.49 NCS extension: 23 residues added (3 deleted due to clashes), 6445 seeds are put forward Round 1: 506 peptides, 82 chains. Longest chain 18 peptides. Score 0.431 Round 2: 535 peptides, 67 chains. Longest chain 25 peptides. Score 0.546 Round 3: 545 peptides, 62 chains. Longest chain 28 peptides. Score 0.582 Round 4: 559 peptides, 64 chains. Longest chain 34 peptides. Score 0.587 Round 5: 569 peptides, 62 chains. Longest chain 34 peptides. Score 0.606 Taking the results from Round 5 Chains 67, Residues 507, Estimated correctness of the model 70.3 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12989 restraints for refining 6443 atoms. 10807 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3004 (Rfree = 0.000) for 6443 atoms. Found 76 (104 requested) and removed 63 (52 requested) atoms. Cycle 7: After refmac, R = 0.2854 (Rfree = 0.000) for 6420 atoms. Found 63 (104 requested) and removed 63 (52 requested) atoms. Cycle 8: After refmac, R = 0.2828 (Rfree = 0.000) for 6394 atoms. Found 66 (104 requested) and removed 72 (52 requested) atoms. Cycle 9: After refmac, R = 0.2766 (Rfree = 0.000) for 6372 atoms. Found 50 (103 requested) and removed 54 (51 requested) atoms. Cycle 10: After refmac, R = 0.2713 (Rfree = 0.000) for 6357 atoms. Found 47 (103 requested) and removed 54 (51 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.90 2.50 NCS extension: 5 residues added (0 deleted due to clashes), 6422 seeds are put forward Round 1: 494 peptides, 69 chains. Longest chain 19 peptides. Score 0.488 Round 2: 530 peptides, 65 chains. Longest chain 23 peptides. Score 0.551 Round 3: 546 peptides, 64 chains. Longest chain 24 peptides. Score 0.573 Round 4: 540 peptides, 64 chains. Longest chain 29 peptides. Score 0.567 Round 5: 542 peptides, 56 chains. Longest chain 32 peptides. Score 0.607 Taking the results from Round 5 Chains 65, Residues 486, Estimated correctness of the model 70.4 % 11 chains (123 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12161 restraints for refining 6444 atoms. 9818 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2889 (Rfree = 0.000) for 6444 atoms. Found 67 (104 requested) and removed 65 (52 requested) atoms. Cycle 12: After refmac, R = 0.2861 (Rfree = 0.000) for 6418 atoms. Found 74 (104 requested) and removed 62 (52 requested) atoms. Cycle 13: After refmac, R = 0.2758 (Rfree = 0.000) for 6410 atoms. Found 69 (104 requested) and removed 53 (52 requested) atoms. Cycle 14: After refmac, R = 0.2704 (Rfree = 0.000) for 6411 atoms. Found 43 (104 requested) and removed 55 (52 requested) atoms. Cycle 15: After refmac, R = 0.2694 (Rfree = 0.000) for 6389 atoms. Found 46 (103 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 2.52 NCS extension: 51 residues added (10 deleted due to clashes), 6468 seeds are put forward Round 1: 516 peptides, 68 chains. Longest chain 29 peptides. Score 0.519 Round 2: 529 peptides, 58 chains. Longest chain 25 peptides. Score 0.584 Round 3: 557 peptides, 65 chains. Longest chain 32 peptides. Score 0.580 Round 4: 549 peptides, 57 chains. Longest chain 31 peptides. Score 0.610 Round 5: 569 peptides, 61 chains. Longest chain 34 peptides. Score 0.611 Taking the results from Round 5 Chains 64, Residues 508, Estimated correctness of the model 70.9 % 7 chains (106 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12566 restraints for refining 6442 atoms. 10206 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2860 (Rfree = 0.000) for 6442 atoms. Found 69 (104 requested) and removed 65 (52 requested) atoms. Cycle 17: After refmac, R = 0.2794 (Rfree = 0.000) for 6430 atoms. Found 63 (104 requested) and removed 65 (52 requested) atoms. Cycle 18: After refmac, R = 0.2644 (Rfree = 0.000) for 6419 atoms. Found 51 (104 requested) and removed 56 (52 requested) atoms. Cycle 19: After refmac, R = 0.2661 (Rfree = 0.000) for 6409 atoms. Found 47 (104 requested) and removed 63 (52 requested) atoms. Cycle 20: After refmac, R = 0.2556 (Rfree = 0.000) for 6392 atoms. Found 43 (103 requested) and removed 52 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 2.51 NCS extension: 41 residues added (5 deleted due to clashes), 6491 seeds are put forward Round 1: 491 peptides, 59 chains. Longest chain 28 peptides. Score 0.538 Round 2: 519 peptides, 56 chains. Longest chain 30 peptides. Score 0.584 Round 3: 550 peptides, 52 chains. Longest chain 48 peptides. Score 0.634 Round 4: 540 peptides, 59 chains. Longest chain 32 peptides. Score 0.591 Round 5: 548 peptides, 55 chains. Longest chain 38 peptides. Score 0.618 Taking the results from Round 3 Chains 55, Residues 498, Estimated correctness of the model 74.0 % 12 chains (184 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 11496 restraints for refining 6440 atoms. 8881 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2852 (Rfree = 0.000) for 6440 atoms. Found 95 (104 requested) and removed 87 (52 requested) atoms. Cycle 22: After refmac, R = 0.2842 (Rfree = 0.000) for 6427 atoms. Found 75 (104 requested) and removed 67 (52 requested) atoms. Cycle 23: After refmac, R = 0.2731 (Rfree = 0.000) for 6424 atoms. Found 71 (104 requested) and removed 55 (52 requested) atoms. Cycle 24: After refmac, R = 0.2698 (Rfree = 0.000) for 6433 atoms. Found 58 (104 requested) and removed 53 (52 requested) atoms. Cycle 25: After refmac, R = 0.2707 (Rfree = 0.000) for 6431 atoms. Found 68 (104 requested) and removed 53 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.95 2.54 NCS extension: 21 residues added (12 deleted due to clashes), 6498 seeds are put forward Round 1: 492 peptides, 64 chains. Longest chain 27 peptides. Score 0.512 Round 2: 534 peptides, 59 chains. Longest chain 27 peptides. Score 0.585 Round 3: 532 peptides, 55 chains. Longest chain 32 peptides. Score 0.602 Round 4: 542 peptides, 56 chains. Longest chain 29 peptides. Score 0.607 Round 5: 566 peptides, 61 chains. Longest chain 31 peptides. Score 0.608 Taking the results from Round 5 Chains 69, Residues 505, Estimated correctness of the model 70.5 % 12 chains (119 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12378 restraints for refining 6443 atoms. 9996 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2922 (Rfree = 0.000) for 6443 atoms. Found 100 (104 requested) and removed 69 (52 requested) atoms. Cycle 27: After refmac, R = 0.2784 (Rfree = 0.000) for 6446 atoms. Found 83 (105 requested) and removed 60 (52 requested) atoms. Cycle 28: After refmac, R = 0.2672 (Rfree = 0.000) for 6458 atoms. Found 63 (104 requested) and removed 54 (52 requested) atoms. Cycle 29: After refmac, R = 0.2622 (Rfree = 0.000) for 6463 atoms. Found 58 (104 requested) and removed 53 (52 requested) atoms. Cycle 30: After refmac, R = 0.2618 (Rfree = 0.000) for 6463 atoms. Found 52 (104 requested) and removed 52 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.92 2.52 NCS extension: 145 residues added (13 deleted due to clashes), 6642 seeds are put forward Round 1: 504 peptides, 68 chains. Longest chain 25 peptides. Score 0.505 Round 2: 539 peptides, 53 chains. Longest chain 38 peptides. Score 0.619 Round 3: 534 peptides, 55 chains. Longest chain 62 peptides. Score 0.604 Round 4: 539 peptides, 52 chains. Longest chain 34 peptides. Score 0.623 Round 5: 534 peptides, 52 chains. Longest chain 40 peptides. Score 0.618 Taking the results from Round 4 Chains 61, Residues 487, Estimated correctness of the model 72.6 % 11 chains (137 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12282 restraints for refining 6444 atoms. 9890 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2842 (Rfree = 0.000) for 6444 atoms. Found 89 (104 requested) and removed 64 (52 requested) atoms. Cycle 32: After refmac, R = 0.2809 (Rfree = 0.000) for 6449 atoms. Found 96 (104 requested) and removed 62 (52 requested) atoms. Cycle 33: After refmac, R = 0.2735 (Rfree = 0.000) for 6469 atoms. Found 62 (105 requested) and removed 54 (52 requested) atoms. Cycle 34: After refmac, R = 0.2695 (Rfree = 0.000) for 6467 atoms. Found 63 (105 requested) and removed 55 (52 requested) atoms. Cycle 35: After refmac, R = 0.2455 (Rfree = 0.000) for 6466 atoms. Found 28 (105 requested) and removed 54 (52 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.92 2.52 NCS extension: 95 residues added (24 deleted due to clashes), 6569 seeds are put forward Round 1: 477 peptides, 61 chains. Longest chain 34 peptides. Score 0.511 Round 2: 509 peptides, 53 chains. Longest chain 36 peptides. Score 0.588 Round 3: 513 peptides, 59 chains. Longest chain 45 peptides. Score 0.562 Round 4: 509 peptides, 53 chains. Longest chain 32 peptides. Score 0.588 Round 5: 519 peptides, 53 chains. Longest chain 38 peptides. Score 0.599 Taking the results from Round 5 Chains 60, Residues 466, Estimated correctness of the model 69.3 % 9 chains (139 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12451 restraints for refining 6444 atoms. 10108 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2944 (Rfree = 0.000) for 6444 atoms. Found 95 (104 requested) and removed 69 (52 requested) atoms. Cycle 37: After refmac, R = 0.2816 (Rfree = 0.000) for 6458 atoms. Found 90 (104 requested) and removed 61 (52 requested) atoms. Cycle 38: After refmac, R = 0.2678 (Rfree = 0.000) for 6478 atoms. Found 61 (105 requested) and removed 57 (52 requested) atoms. Cycle 39: After refmac, R = 0.2473 (Rfree = 0.000) for 6474 atoms. Found 29 (105 requested) and removed 54 (52 requested) atoms. Cycle 40: After refmac, R = 0.2531 (Rfree = 0.000) for 6448 atoms. Found 46 (104 requested) and removed 53 (52 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.90 2.50 NCS extension: 418 residues added (40 deleted due to clashes), 6900 seeds are put forward Round 1: 482 peptides, 57 chains. Longest chain 29 peptides. Score 0.538 Round 2: 488 peptides, 51 chains. Longest chain 25 peptides. Score 0.576 Round 3: 505 peptides, 52 chains. Longest chain 37 peptides. Score 0.589 Round 4: 497 peptides, 48 chains. Longest chain 38 peptides. Score 0.600 Round 5: 503 peptides, 55 chains. Longest chain 31 peptides. Score 0.572 Taking the results from Round 4 Chains 55, Residues 449, Estimated correctness of the model 69.4 % 8 chains (118 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 12810 restraints for refining 6444 atoms. 10609 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2768 (Rfree = 0.000) for 6444 atoms. Found 71 (104 requested) and removed 66 (52 requested) atoms. Cycle 42: After refmac, R = 0.2632 (Rfree = 0.000) for 6434 atoms. Found 62 (104 requested) and removed 55 (52 requested) atoms. Cycle 43: After refmac, R = 0.2639 (Rfree = 0.000) for 6426 atoms. Found 62 (104 requested) and removed 52 (52 requested) atoms. Cycle 44: After refmac, R = 0.2582 (Rfree = 0.000) for 6427 atoms. Found 63 (104 requested) and removed 52 (52 requested) atoms. Cycle 45: After refmac, R = 0.2556 (Rfree = 0.000) for 6427 atoms. Found 67 (104 requested) and removed 52 (52 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.89 2.49 NCS extension: 210 residues added (31 deleted due to clashes), 6685 seeds are put forward Round 1: 450 peptides, 56 chains. Longest chain 27 peptides. Score 0.506 Round 2: 483 peptides, 52 chains. Longest chain 27 peptides. Score 0.565 Round 3: 500 peptides, 49 chains. Longest chain 30 peptides. Score 0.599 Round 4: 483 peptides, 49 chains. Longest chain 33 peptides. Score 0.581 Round 5: 494 peptides, 50 chains. Longest chain 32 peptides. Score 0.587 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 451, Estimated correctness of the model 69.3 % 11 chains (126 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 2gvh-2_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (451 residues) following loop building 11 chains (126 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 32893 reflections ( 89.68 % complete ) and 12561 restraints for refining 6444 atoms. 10368 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2720 (Rfree = 0.000) for 6444 atoms. Found 0 (104 requested) and removed 52 (52 requested) atoms. Cycle 47: After refmac, R = 0.2671 (Rfree = 0.000) for 6378 atoms. Found 0 (103 requested) and removed 28 (51 requested) atoms. Cycle 48: After refmac, R = 0.2558 (Rfree = 0.000) for 6347 atoms. Found 0 (102 requested) and removed 31 (51 requested) atoms. Cycle 49: After refmac, R = 0.2489 (Rfree = 0.000) for 6310 atoms. Found 0 (102 requested) and removed 17 (51 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:10:57 GMT 2018 Job finished. TimeTaking 76.05 Used memory is bytes: 8460872