Mon 24 Dec 07:35:44 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 2f4l-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-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 07:35:48 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/2f4l-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-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 895 and 0 Target number of residues in the AU: 895 Target solvent content: 0.6248 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 9504 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: 86.372 3.200 Wilson plot Bfac: 63.68 21953 reflections ( 99.76 % complete ) and 0 restraints for refining 10534 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3347 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2810 (Rfree = 0.000) for 10534 atoms. Found 59 (94 requested) and removed 296 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 10381 seeds are put forward NCS extension: 0 residues added, 10381 seeds are put forward Round 1: 475 peptides, 99 chains. Longest chain 11 peptides. Score 0.282 Round 2: 591 peptides, 104 chains. Longest chain 14 peptides. Score 0.405 Round 3: 633 peptides, 107 chains. Longest chain 16 peptides. Score 0.440 Round 4: 649 peptides, 107 chains. Longest chain 15 peptides. Score 0.458 Round 5: 694 peptides, 107 chains. Longest chain 19 peptides. Score 0.508 Taking the results from Round 5 Chains 112, Residues 587, Estimated correctness of the model 13.9 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 18716 restraints for refining 8676 atoms. 16329 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2676 (Rfree = 0.000) for 8676 atoms. Found 77 (77 requested) and removed 103 (38 requested) atoms. Cycle 2: After refmac, R = 0.2605 (Rfree = 0.000) for 8549 atoms. Found 51 (77 requested) and removed 57 (38 requested) atoms. Cycle 3: After refmac, R = 0.2574 (Rfree = 0.000) for 8508 atoms. Found 36 (76 requested) and removed 51 (38 requested) atoms. Cycle 4: After refmac, R = 0.2478 (Rfree = 0.000) for 8470 atoms. Found 22 (76 requested) and removed 45 (38 requested) atoms. Cycle 5: After refmac, R = 0.2446 (Rfree = 0.000) for 8435 atoms. Found 36 (75 requested) and removed 55 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.15 Search for helices and strands: 0 residues in 0 chains, 8620 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 8651 seeds are put forward Round 1: 630 peptides, 98 chains. Longest chain 22 peptides. Score 0.481 Round 2: 717 peptides, 101 chains. Longest chain 29 peptides. Score 0.559 Round 3: 704 peptides, 98 chains. Longest chain 24 peptides. Score 0.559 Round 4: 716 peptides, 86 chains. Longest chain 25 peptides. Score 0.620 Round 5: 737 peptides, 87 chains. Longest chain 41 peptides. Score 0.635 Taking the results from Round 5 Chains 94, Residues 650, Estimated correctness of the model 50.2 % 6 chains (77 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 18426 restraints for refining 8676 atoms. 15645 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 8676 atoms. Found 52 (77 requested) and removed 70 (38 requested) atoms. Cycle 7: After refmac, R = 0.2468 (Rfree = 0.000) for 8607 atoms. Found 26 (77 requested) and removed 45 (38 requested) atoms. Cycle 8: After refmac, R = 0.2447 (Rfree = 0.000) for 8562 atoms. Found 20 (77 requested) and removed 47 (38 requested) atoms. Cycle 9: After refmac, R = 0.2409 (Rfree = 0.000) for 8519 atoms. Found 20 (76 requested) and removed 47 (38 requested) atoms. Cycle 10: After refmac, R = 0.2404 (Rfree = 0.000) for 8477 atoms. Found 17 (76 requested) and removed 47 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 8625 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8640 seeds are put forward Round 1: 678 peptides, 105 chains. Longest chain 22 peptides. Score 0.500 Round 2: 717 peptides, 98 chains. Longest chain 23 peptides. Score 0.571 Round 3: 717 peptides, 89 chains. Longest chain 40 peptides. Score 0.609 Round 4: 710 peptides, 88 chains. Longest chain 23 peptides. Score 0.607 Round 5: 733 peptides, 87 chains. Longest chain 34 peptides. Score 0.631 Taking the results from Round 5 Chains 91, Residues 646, Estimated correctness of the model 49.1 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 18586 restraints for refining 8676 atoms. 15921 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2569 (Rfree = 0.000) for 8676 atoms. Found 69 (77 requested) and removed 65 (38 requested) atoms. Cycle 12: After refmac, R = 0.2346 (Rfree = 0.000) for 8637 atoms. Found 38 (77 requested) and removed 44 (38 requested) atoms. Cycle 13: After refmac, R = 0.2314 (Rfree = 0.000) for 8605 atoms. Found 25 (77 requested) and removed 45 (38 requested) atoms. Cycle 14: After refmac, R = 0.2350 (Rfree = 0.000) for 8567 atoms. Found 21 (77 requested) and removed 46 (38 requested) atoms. Cycle 15: After refmac, R = 0.2296 (Rfree = 0.000) for 8508 atoms. Found 32 (76 requested) and removed 47 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 8631 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 8656 seeds are put forward Round 1: 657 peptides, 102 chains. Longest chain 23 peptides. Score 0.491 Round 2: 705 peptides, 91 chains. Longest chain 48 peptides. Score 0.590 Round 3: 725 peptides, 90 chains. Longest chain 33 peptides. Score 0.612 Round 4: 707 peptides, 90 chains. Longest chain 38 peptides. Score 0.596 Round 5: 739 peptides, 91 chains. Longest chain 24 peptides. Score 0.621 Taking the results from Round 5 Chains 95, Residues 648, Estimated correctness of the model 46.6 % 7 chains (49 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 18706 restraints for refining 8674 atoms. 16052 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2481 (Rfree = 0.000) for 8674 atoms. Found 54 (77 requested) and removed 52 (38 requested) atoms. Cycle 17: After refmac, R = 0.2278 (Rfree = 0.000) for 8648 atoms. Found 20 (77 requested) and removed 50 (38 requested) atoms. Cycle 18: After refmac, R = 0.2274 (Rfree = 0.000) for 8593 atoms. Found 28 (77 requested) and removed 46 (38 requested) atoms. Cycle 19: After refmac, R = 0.2155 (Rfree = 0.000) for 8550 atoms. Found 19 (76 requested) and removed 47 (38 requested) atoms. Cycle 20: After refmac, R = 0.2148 (Rfree = 0.000) for 8501 atoms. Found 41 (76 requested) and removed 42 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8681 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 8703 seeds are put forward Round 1: 616 peptides, 98 chains. Longest chain 20 peptides. Score 0.465 Round 2: 705 peptides, 92 chains. Longest chain 25 peptides. Score 0.586 Round 3: 672 peptides, 86 chains. Longest chain 25 peptides. Score 0.580 Round 4: 707 peptides, 90 chains. Longest chain 26 peptides. Score 0.596 Round 5: 681 peptides, 85 chains. Longest chain 23 peptides. Score 0.593 Taking the results from Round 4 Chains 96, Residues 617, Estimated correctness of the model 40.0 % 10 chains (87 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 18380 restraints for refining 8675 atoms. 15723 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2416 (Rfree = 0.000) for 8675 atoms. Found 46 (77 requested) and removed 50 (38 requested) atoms. Cycle 22: After refmac, R = 0.2309 (Rfree = 0.000) for 8635 atoms. Found 33 (77 requested) and removed 42 (38 requested) atoms. Cycle 23: After refmac, R = 0.2218 (Rfree = 0.000) for 8601 atoms. Found 21 (77 requested) and removed 45 (38 requested) atoms. Cycle 24: After refmac, R = 0.2619 (Rfree = 0.000) for 8555 atoms. Found 69 (76 requested) and removed 51 (38 requested) atoms. Cycle 25: After refmac, R = 0.2116 (Rfree = 0.000) for 8553 atoms. Found 32 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.19 Search for helices and strands: 0 residues in 0 chains, 8672 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 8687 seeds are put forward Round 1: 605 peptides, 101 chains. Longest chain 25 peptides. Score 0.437 Round 2: 672 peptides, 100 chains. Longest chain 22 peptides. Score 0.517 Round 3: 664 peptides, 90 chains. Longest chain 24 peptides. Score 0.554 Round 4: 688 peptides, 95 chains. Longest chain 28 peptides. Score 0.556 Round 5: 709 peptides, 95 chains. Longest chain 26 peptides. Score 0.577 Taking the results from Round 5 Chains 96, Residues 614, Estimated correctness of the model 34.7 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 18489 restraints for refining 8675 atoms. 15862 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2437 (Rfree = 0.000) for 8675 atoms. Found 66 (77 requested) and removed 53 (38 requested) atoms. Cycle 27: After refmac, R = 0.2301 (Rfree = 0.000) for 8652 atoms. Found 27 (77 requested) and removed 40 (38 requested) atoms. Cycle 28: After refmac, R = 0.2275 (Rfree = 0.000) for 8622 atoms. Found 29 (77 requested) and removed 43 (38 requested) atoms. Cycle 29: After refmac, R = 0.2243 (Rfree = 0.000) for 8592 atoms. Found 26 (77 requested) and removed 41 (38 requested) atoms. Cycle 30: After refmac, R = 0.2228 (Rfree = 0.000) for 8562 atoms. Found 28 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8695 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 8718 seeds are put forward Round 1: 596 peptides, 101 chains. Longest chain 24 peptides. Score 0.427 Round 2: 646 peptides, 92 chains. Longest chain 24 peptides. Score 0.527 Round 3: 669 peptides, 94 chains. Longest chain 21 peptides. Score 0.541 Round 4: 659 peptides, 87 chains. Longest chain 27 peptides. Score 0.563 Round 5: 640 peptides, 90 chains. Longest chain 21 peptides. Score 0.530 Taking the results from Round 4 Chains 89, Residues 572, Estimated correctness of the model 30.7 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 19185 restraints for refining 8674 atoms. 16843 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2415 (Rfree = 0.000) for 8674 atoms. Found 76 (77 requested) and removed 53 (38 requested) atoms. Cycle 32: After refmac, R = 0.2268 (Rfree = 0.000) for 8663 atoms. Found 38 (78 requested) and removed 42 (39 requested) atoms. Cycle 33: After refmac, R = 0.2291 (Rfree = 0.000) for 8634 atoms. Found 39 (77 requested) and removed 43 (38 requested) atoms. Cycle 34: After refmac, R = 0.2384 (Rfree = 0.000) for 8612 atoms. Found 62 (77 requested) and removed 42 (38 requested) atoms. Cycle 35: After refmac, R = 0.2461 (Rfree = 0.000) for 8607 atoms. Found 55 (77 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.14 Search for helices and strands: 0 residues in 0 chains, 8746 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 8769 seeds are put forward Round 1: 535 peptides, 101 chains. Longest chain 14 peptides. Score 0.351 Round 2: 602 peptides, 93 chains. Longest chain 19 peptides. Score 0.474 Round 3: 601 peptides, 95 chains. Longest chain 20 peptides. Score 0.463 Round 4: 588 peptides, 87 chains. Longest chain 24 peptides. Score 0.488 Round 5: 601 peptides, 89 chains. Longest chain 20 peptides. Score 0.492 Taking the results from Round 5 Chains 89, Residues 512, Estimated correctness of the model 8.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 19800 restraints for refining 8675 atoms. 17825 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2404 (Rfree = 0.000) for 8675 atoms. Found 66 (77 requested) and removed 43 (38 requested) atoms. Cycle 37: After refmac, R = 0.2287 (Rfree = 0.000) for 8672 atoms. Found 38 (78 requested) and removed 43 (39 requested) atoms. Cycle 38: After refmac, R = 0.2574 (Rfree = 0.000) for 8650 atoms. Found 66 (77 requested) and removed 117 (38 requested) atoms. Cycle 39: After refmac, R = 0.2465 (Rfree = 0.000) for 8584 atoms. Found 57 (77 requested) and removed 61 (38 requested) atoms. Cycle 40: After refmac, R = 0.2173 (Rfree = 0.000) for 8561 atoms. Found 19 (77 requested) and removed 49 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8661 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8682 seeds are put forward Round 1: 491 peptides, 96 chains. Longest chain 15 peptides. Score 0.321 Round 2: 549 peptides, 90 chains. Longest chain 22 peptides. Score 0.427 Round 3: 555 peptides, 86 chains. Longest chain 22 peptides. Score 0.455 Round 4: 560 peptides, 91 chains. Longest chain 18 peptides. Score 0.435 Round 5: 532 peptides, 85 chains. Longest chain 19 peptides. Score 0.433 Taking the results from Round 3 Chains 86, Residues 469, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 19569 restraints for refining 8599 atoms. 17707 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2375 (Rfree = 0.000) for 8599 atoms. Found 62 (77 requested) and removed 51 (38 requested) atoms. Cycle 42: After refmac, R = 0.2495 (Rfree = 0.000) for 8587 atoms. Found 77 (77 requested) and removed 51 (38 requested) atoms. Cycle 43: After refmac, R = 0.2286 (Rfree = 0.000) for 8584 atoms. Found 60 (77 requested) and removed 45 (38 requested) atoms. Cycle 44: After refmac, R = 0.2048 (Rfree = 0.000) for 8570 atoms. Found 22 (77 requested) and removed 40 (38 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2564 (Rfree = 0.000) for 8545 atoms. Found 76 (76 requested) and removed 46 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.12 Search for helices and strands: 0 residues in 0 chains, 8713 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 8748 seeds are put forward Round 1: 478 peptides, 95 chains. Longest chain 13 peptides. Score 0.309 Round 2: 530 peptides, 92 chains. Longest chain 16 peptides. Score 0.393 Round 3: 584 peptides, 90 chains. Longest chain 18 peptides. Score 0.468 Round 4: 558 peptides, 92 chains. Longest chain 15 peptides. Score 0.428 Round 5: 581 peptides, 93 chains. Longest chain 19 peptides. Score 0.450 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 90, Residues 494, Estimated correctness of the model 0.7 % 4 chains (15 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 90 chains (494 residues) following loop building 4 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21953 reflections ( 99.76 % complete ) and 19284 restraints for refining 8595 atoms. 17368 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2279 (Rfree = 0.000) for 8595 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.2202 (Rfree = 0.000) for 8519 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.2222 (Rfree = 0.000) for 8475 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 49: After refmac, R = 0.2183 (Rfree = 0.000) for 8431 atoms. TimeTaking 84.55