Mon 24 Dec 07:47:07 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 1vl5-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-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/1vl5-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-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 07:47:12 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/1vl5-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.4-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 813 and 0 Target number of residues in the AU: 813 Target solvent content: 0.6202 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.4-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: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 3.400 Wilson plot Bfac: 61.39 15845 reflections ( 99.92 % complete ) and 0 restraints for refining 9204 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3250 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 9204 atoms. Found 69 (69 requested) and removed 92 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 9315 seeds are put forward NCS extension: 0 residues added, 9315 seeds are put forward Round 1: 447 peptides, 87 chains. Longest chain 13 peptides. Score 0.325 Round 2: 570 peptides, 89 chains. Longest chain 16 peptides. Score 0.481 Round 3: 591 peptides, 83 chains. Longest chain 16 peptides. Score 0.538 Round 4: 606 peptides, 80 chains. Longest chain 21 peptides. Score 0.569 Round 5: 632 peptides, 85 chains. Longest chain 23 peptides. Score 0.573 Taking the results from Round 5 Chains 86, Residues 547, Estimated correctness of the model 19.6 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16518 restraints for refining 7565 atoms. 14276 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2427 (Rfree = 0.000) for 7565 atoms. Found 45 (57 requested) and removed 58 (28 requested) atoms. Cycle 2: After refmac, R = 0.2343 (Rfree = 0.000) for 7429 atoms. Found 27 (57 requested) and removed 43 (28 requested) atoms. Cycle 3: After refmac, R = 0.2185 (Rfree = 0.000) for 7355 atoms. Found 23 (55 requested) and removed 44 (27 requested) atoms. Cycle 4: After refmac, R = 0.2136 (Rfree = 0.000) for 7294 atoms. Found 13 (55 requested) and removed 38 (27 requested) atoms. Cycle 5: After refmac, R = 0.2023 (Rfree = 0.000) for 7238 atoms. Found 11 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7470 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7493 seeds are put forward Round 1: 541 peptides, 90 chains. Longest chain 20 peptides. Score 0.438 Round 2: 571 peptides, 83 chains. Longest chain 18 peptides. Score 0.514 Round 3: 601 peptides, 80 chains. Longest chain 21 peptides. Score 0.564 Round 4: 602 peptides, 79 chains. Longest chain 24 peptides. Score 0.570 Round 5: 614 peptides, 84 chains. Longest chain 26 peptides. Score 0.559 Taking the results from Round 4 Chains 82, Residues 523, Estimated correctness of the model 18.6 % 7 chains (64 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15928 restraints for refining 7480 atoms. 13710 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2295 (Rfree = 0.000) for 7480 atoms. Found 33 (56 requested) and removed 57 (28 requested) atoms. Cycle 7: After refmac, R = 0.2149 (Rfree = 0.000) for 7394 atoms. Found 14 (56 requested) and removed 35 (28 requested) atoms. Cycle 8: After refmac, R = 0.2077 (Rfree = 0.000) for 7330 atoms. Found 25 (55 requested) and removed 44 (27 requested) atoms. Cycle 9: After refmac, R = 0.1989 (Rfree = 0.000) for 7294 atoms. Found 17 (55 requested) and removed 38 (27 requested) atoms. Cycle 10: After refmac, R = 0.1958 (Rfree = 0.000) for 7258 atoms. Found 15 (54 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7505 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 7529 seeds are put forward Round 1: 519 peptides, 85 chains. Longest chain 14 peptides. Score 0.438 Round 2: 558 peptides, 89 chains. Longest chain 13 peptides. Score 0.466 Round 3: 579 peptides, 82 chains. Longest chain 21 peptides. Score 0.529 Round 4: 575 peptides, 78 chains. Longest chain 26 peptides. Score 0.545 Round 5: 569 peptides, 76 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 5 Chains 76, Residues 493, Estimated correctness of the model 10.8 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16748 restraints for refining 7565 atoms. 14658 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2306 (Rfree = 0.000) for 7565 atoms. Found 38 (57 requested) and removed 47 (28 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2213 (Rfree = 0.000) for 7514 atoms. Found 29 (57 requested) and removed 41 (28 requested) atoms. Cycle 13: After refmac, R = 0.2115 (Rfree = 0.000) for 7475 atoms. Found 24 (56 requested) and removed 37 (28 requested) atoms. Cycle 14: After refmac, R = 0.2061 (Rfree = 0.000) for 7441 atoms. Found 31 (56 requested) and removed 39 (28 requested) atoms. Cycle 15: After refmac, R = 0.1973 (Rfree = 0.000) for 7413 atoms. Found 24 (56 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7637 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 7652 seeds are put forward Round 1: 506 peptides, 86 chains. Longest chain 16 peptides. Score 0.415 Round 2: 570 peptides, 81 chains. Longest chain 16 peptides. Score 0.524 Round 3: 596 peptides, 75 chains. Longest chain 21 peptides. Score 0.583 Round 4: 590 peptides, 79 chains. Longest chain 21 peptides. Score 0.557 Round 5: 573 peptides, 73 chains. Longest chain 21 peptides. Score 0.568 Taking the results from Round 3 Chains 78, Residues 521, Estimated correctness of the model 23.0 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 15885 restraints for refining 7562 atoms. 13631 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2304 (Rfree = 0.000) for 7562 atoms. Found 41 (57 requested) and removed 53 (28 requested) atoms. Cycle 17: After refmac, R = 0.2180 (Rfree = 0.000) for 7497 atoms. Found 26 (57 requested) and removed 38 (28 requested) atoms. Cycle 18: After refmac, R = 0.2111 (Rfree = 0.000) for 7455 atoms. Found 29 (56 requested) and removed 39 (28 requested) atoms. Cycle 19: After refmac, R = 0.2032 (Rfree = 0.000) for 7423 atoms. Found 19 (56 requested) and removed 33 (28 requested) atoms. Cycle 20: After refmac, R = 0.2028 (Rfree = 0.000) for 7395 atoms. Found 32 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7666 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7686 seeds are put forward Round 1: 493 peptides, 85 chains. Longest chain 13 peptides. Score 0.403 Round 2: 538 peptides, 81 chains. Longest chain 17 peptides. Score 0.485 Round 3: 535 peptides, 74 chains. Longest chain 21 peptides. Score 0.519 Round 4: 535 peptides, 70 chains. Longest chain 26 peptides. Score 0.540 Round 5: 542 peptides, 69 chains. Longest chain 22 peptides. Score 0.553 Taking the results from Round 5 Chains 70, Residues 473, Estimated correctness of the model 12.6 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 16828 restraints for refining 7565 atoms. 14827 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2303 (Rfree = 0.000) for 7565 atoms. Found 41 (57 requested) and removed 44 (28 requested) atoms. Cycle 22: After refmac, R = 0.2252 (Rfree = 0.000) for 7521 atoms. Found 36 (57 requested) and removed 36 (28 requested) atoms. Cycle 23: After refmac, R = 0.2062 (Rfree = 0.000) for 7495 atoms. Found 25 (56 requested) and removed 36 (28 requested) atoms. Cycle 24: After refmac, R = 0.2006 (Rfree = 0.000) for 7468 atoms. Found 24 (56 requested) and removed 37 (28 requested) atoms. Cycle 25: After refmac, R = 0.1925 (Rfree = 0.000) for 7439 atoms. Found 19 (56 requested) and removed 39 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 7671 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7687 seeds are put forward Round 1: 471 peptides, 82 chains. Longest chain 18 peptides. Score 0.390 Round 2: 490 peptides, 78 chains. Longest chain 21 peptides. Score 0.440 Round 3: 522 peptides, 79 chains. Longest chain 16 peptides. Score 0.476 Round 4: 526 peptides, 78 chains. Longest chain 27 peptides. Score 0.486 Round 5: 535 peptides, 81 chains. Longest chain 15 peptides. Score 0.481 Taking the results from Round 4 Chains 78, Residues 448, Estimated correctness of the model 0.0 % 4 chains (12 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 17279 restraints for refining 7564 atoms. 15540 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2180 (Rfree = 0.000) for 7564 atoms. Found 26 (57 requested) and removed 35 (28 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 7520 atoms. Found 36 (57 requested) and removed 34 (28 requested) atoms. Cycle 28: After refmac, R = 0.2027 (Rfree = 0.000) for 7499 atoms. Found 27 (56 requested) and removed 32 (28 requested) atoms. Cycle 29: After refmac, R = 0.1959 (Rfree = 0.000) for 7487 atoms. Found 16 (56 requested) and removed 34 (28 requested) atoms. Cycle 30: After refmac, R = 0.1978 (Rfree = 0.000) for 7462 atoms. Found 23 (56 requested) and removed 39 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7707 seeds are put forward NCS extension: 28 residues added (7 deleted due to clashes), 7735 seeds are put forward Round 1: 449 peptides, 83 chains. Longest chain 18 peptides. Score 0.353 Round 2: 477 peptides, 79 chains. Longest chain 18 peptides. Score 0.417 Round 3: 482 peptides, 76 chains. Longest chain 22 peptides. Score 0.441 Round 4: 475 peptides, 72 chains. Longest chain 21 peptides. Score 0.455 Round 5: 466 peptides, 75 chains. Longest chain 16 peptides. Score 0.425 Taking the results from Round 4 Chains 73, Residues 403, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 17561 restraints for refining 7564 atoms. 15983 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2025 (Rfree = 0.000) for 7564 atoms. Found 34 (57 requested) and removed 34 (28 requested) atoms. Cycle 32: After refmac, R = 0.1886 (Rfree = 0.000) for 7536 atoms. Found 18 (57 requested) and removed 33 (28 requested) atoms. Cycle 33: After refmac, R = 0.1808 (Rfree = 0.000) for 7507 atoms. Found 24 (56 requested) and removed 29 (28 requested) atoms. Cycle 34: After refmac, R = 0.1778 (Rfree = 0.000) for 7493 atoms. Found 19 (56 requested) and removed 34 (28 requested) atoms. Cycle 35: After refmac, R = 0.1768 (Rfree = 0.000) for 7470 atoms. Found 20 (56 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7692 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 7716 seeds are put forward Round 1: 405 peptides, 81 chains. Longest chain 11 peptides. Score 0.300 Round 2: 457 peptides, 77 chains. Longest chain 13 peptides. Score 0.401 Round 3: 443 peptides, 70 chains. Longest chain 14 peptides. Score 0.424 Round 4: 444 peptides, 70 chains. Longest chain 16 peptides. Score 0.425 Round 5: 452 peptides, 70 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 5 Chains 70, Residues 382, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 17458 restraints for refining 7565 atoms. 15906 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2234 (Rfree = 0.000) for 7565 atoms. Found 36 (57 requested) and removed 50 (28 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1947 (Rfree = 0.000) for 7522 atoms. Found 20 (57 requested) and removed 36 (28 requested) atoms. Cycle 38: After refmac, R = 0.1935 (Rfree = 0.000) for 7487 atoms. Found 26 (56 requested) and removed 36 (28 requested) atoms. Cycle 39: After refmac, R = 0.1908 (Rfree = 0.000) for 7472 atoms. Found 31 (56 requested) and removed 31 (28 requested) atoms. Cycle 40: After refmac, R = 0.1810 (Rfree = 0.000) for 7463 atoms. Found 16 (56 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 7642 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 7653 seeds are put forward Round 1: 424 peptides, 83 chains. Longest chain 13 peptides. Score 0.316 Round 2: 464 peptides, 75 chains. Longest chain 15 peptides. Score 0.423 Round 3: 465 peptides, 76 chains. Longest chain 23 peptides. Score 0.418 Round 4: 466 peptides, 71 chains. Longest chain 15 peptides. Score 0.449 Round 5: 483 peptides, 72 chains. Longest chain 20 peptides. Score 0.465 Taking the results from Round 5 Chains 75, Residues 411, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 15845 reflections ( 99.92 % complete ) and 17230 restraints for refining 7564 atoms. 15591 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2059 (Rfree = 0.000) for 7564 atoms. Found 34 (57 requested) and removed 37 (28 requested) atoms. Cycle 42: After refmac, R = 0.1900 (Rfree = 0.000) for 7533 atoms. Found 20 (57 requested) and removed 30 (28 requested) atoms. Cycle 43: After refmac, R = 0.1909 (Rfree = 0.000) for 7502 atoms. Found 21 (56 requested) and removed 32 (28 requested) atoms. Cycle 44: After refmac, R = 0.1784 (Rfree = 0.000) for 7480 atoms. Found 13 (56 requested) and removed 32 (28 requested) atoms. Cycle 45: After refmac, R = 0.1764 (Rfree = 0.000) for 7455 atoms. Found 15 (56 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 7642 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7667 seeds are put forward Round 1: 413 peptides, 73 chains. Longest chain 11 peptides. Score 0.363 Round 2: 421 peptides, 70 chains. Longest chain 13 peptides. Score 0.393 Round 3: 444 peptides, 69 chains. Longest chain 18 peptides. Score 0.431 Round 4: 454 peptides, 72 chains. Longest chain 18 peptides. Score 0.427 Round 5: 440 peptides, 67 chains. Longest chain 18 peptides. Score 0.438 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 373, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (373 residues) following loop building 4 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15845 reflections ( 99.92 % complete ) and 17455 restraints for refining 7563 atoms. 15990 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1963 (Rfree = 0.000) for 7563 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.2013 (Rfree = 0.000) for 7518 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.1859 (Rfree = 0.000) for 7489 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.1845 (Rfree = 0.000) for 7456 atoms. TimeTaking 74