Mon 24 Dec 07:29:23 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 1vlu-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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/1vlu-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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 07:29:28 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/1vlu-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.6-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 975 and 0 Target number of residues in the AU: 975 Target solvent content: 0.6410 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-3.6-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.90 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: 44.569 3.600 Wilson plot Bfac: 72.53 17421 reflections ( 99.85 % complete ) and 0 restraints for refining 8261 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3412 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 8261 atoms. Found 52 (52 requested) and removed 78 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 2.80 Search for helices and strands: 0 residues in 0 chains, 8425 seeds are put forward NCS extension: 0 residues added, 8425 seeds are put forward Round 1: 454 peptides, 68 chains. Longest chain 14 peptides. Score 0.407 Round 2: 530 peptides, 61 chains. Longest chain 19 peptides. Score 0.520 Round 3: 532 peptides, 57 chains. Longest chain 22 peptides. Score 0.540 Round 4: 541 peptides, 57 chains. Longest chain 24 peptides. Score 0.549 Round 5: 554 peptides, 62 chains. Longest chain 34 peptides. Score 0.539 Taking the results from Round 4 Chains 62, Residues 484, Estimated correctness of the model 0.0 % 9 chains (127 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14152 restraints for refining 6786 atoms. 11823 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2587 (Rfree = 0.000) for 6786 atoms. Found 43 (43 requested) and removed 67 (21 requested) atoms. Cycle 2: After refmac, R = 0.2406 (Rfree = 0.000) for 6597 atoms. Found 37 (43 requested) and removed 39 (21 requested) atoms. Cycle 3: After refmac, R = 0.2343 (Rfree = 0.000) for 6508 atoms. Found 28 (42 requested) and removed 35 (21 requested) atoms. Cycle 4: After refmac, R = 0.2288 (Rfree = 0.000) for 6432 atoms. Found 28 (41 requested) and removed 32 (20 requested) atoms. Cycle 5: After refmac, R = 0.2253 (Rfree = 0.000) for 6387 atoms. Found 19 (41 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.73 Search for helices and strands: 0 residues in 0 chains, 6637 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 6651 seeds are put forward Round 1: 511 peptides, 66 chains. Longest chain 19 peptides. Score 0.478 Round 2: 558 peptides, 60 chains. Longest chain 32 peptides. Score 0.551 Round 3: 576 peptides, 59 chains. Longest chain 41 peptides. Score 0.572 Round 4: 554 peptides, 53 chains. Longest chain 37 peptides. Score 0.578 Round 5: 569 peptides, 63 chains. Longest chain 35 peptides. Score 0.548 Taking the results from Round 4 Chains 56, Residues 501, Estimated correctness of the model 5.9 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14588 restraints for refining 6677 atoms. 12458 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2690 (Rfree = 0.000) for 6677 atoms. Found 42 (42 requested) and removed 88 (21 requested) atoms. Cycle 7: After refmac, R = 0.2419 (Rfree = 0.000) for 6535 atoms. Found 40 (42 requested) and removed 38 (21 requested) atoms. Cycle 8: After refmac, R = 0.2316 (Rfree = 0.000) for 6496 atoms. Found 33 (41 requested) and removed 39 (20 requested) atoms. Cycle 9: After refmac, R = 0.2231 (Rfree = 0.000) for 6464 atoms. Found 21 (41 requested) and removed 32 (20 requested) atoms. Cycle 10: After refmac, R = 0.2231 (Rfree = 0.000) for 6425 atoms. Found 32 (41 requested) and removed 36 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.75 Search for helices and strands: 0 residues in 0 chains, 6624 seeds are put forward NCS extension: 35 residues added (10 deleted due to clashes), 6659 seeds are put forward Round 1: 522 peptides, 70 chains. Longest chain 17 peptides. Score 0.471 Round 2: 573 peptides, 65 chains. Longest chain 28 peptides. Score 0.543 Round 3: 565 peptides, 63 chains. Longest chain 29 peptides. Score 0.545 Round 4: 561 peptides, 59 chains. Longest chain 33 peptides. Score 0.558 Round 5: 561 peptides, 59 chains. Longest chain 35 peptides. Score 0.558 Taking the results from Round 5 Chains 64, Residues 502, Estimated correctness of the model 0.0 % 6 chains (71 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14619 restraints for refining 6786 atoms. 12430 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2621 (Rfree = 0.000) for 6786 atoms. Found 43 (43 requested) and removed 51 (21 requested) atoms. Cycle 12: After refmac, R = 0.2437 (Rfree = 0.000) for 6692 atoms. Found 43 (43 requested) and removed 51 (21 requested) atoms. Cycle 13: After refmac, R = 0.2309 (Rfree = 0.000) for 6651 atoms. Found 25 (42 requested) and removed 32 (21 requested) atoms. Cycle 14: After refmac, R = 0.2261 (Rfree = 0.000) for 6616 atoms. Found 19 (42 requested) and removed 29 (21 requested) atoms. Cycle 15: After refmac, R = 0.2223 (Rfree = 0.000) for 6583 atoms. Found 28 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.76 Search for helices and strands: 0 residues in 0 chains, 6854 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6872 seeds are put forward Round 1: 534 peptides, 70 chains. Longest chain 27 peptides. Score 0.483 Round 2: 550 peptides, 62 chains. Longest chain 30 peptides. Score 0.535 Round 3: 581 peptides, 62 chains. Longest chain 39 peptides. Score 0.564 Round 4: 577 peptides, 59 chains. Longest chain 32 peptides. Score 0.573 Round 5: 577 peptides, 63 chains. Longest chain 32 peptides. Score 0.556 Taking the results from Round 4 Chains 62, Residues 518, Estimated correctness of the model 3.8 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14697 restraints for refining 6787 atoms. 12599 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2562 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 53 (21 requested) atoms. Cycle 17: After refmac, R = 0.2417 (Rfree = 0.000) for 6709 atoms. Found 39 (43 requested) and removed 40 (21 requested) atoms. Cycle 18: After refmac, R = 0.2323 (Rfree = 0.000) for 6681 atoms. Found 22 (43 requested) and removed 35 (21 requested) atoms. Cycle 19: After refmac, R = 0.2295 (Rfree = 0.000) for 6652 atoms. Found 15 (42 requested) and removed 33 (21 requested) atoms. Cycle 20: After refmac, R = 0.2228 (Rfree = 0.000) for 6620 atoms. Found 13 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.77 Search for helices and strands: 0 residues in 0 chains, 6853 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6872 seeds are put forward Round 1: 537 peptides, 72 chains. Longest chain 18 peptides. Score 0.477 Round 2: 576 peptides, 65 chains. Longest chain 33 peptides. Score 0.546 Round 3: 567 peptides, 65 chains. Longest chain 27 peptides. Score 0.538 Round 4: 571 peptides, 63 chains. Longest chain 36 peptides. Score 0.550 Round 5: 570 peptides, 65 chains. Longest chain 26 peptides. Score 0.541 Taking the results from Round 4 Chains 73, Residues 508, Estimated correctness of the model 0.0 % 7 chains (78 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14230 restraints for refining 6787 atoms. 11991 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2506 (Rfree = 0.000) for 6787 atoms. Found 43 (43 requested) and removed 43 (21 requested) atoms. Cycle 22: After refmac, R = 0.2347 (Rfree = 0.000) for 6728 atoms. Found 32 (43 requested) and removed 27 (21 requested) atoms. Cycle 23: After refmac, R = 0.2293 (Rfree = 0.000) for 6693 atoms. Found 25 (43 requested) and removed 38 (21 requested) atoms. Cycle 24: After refmac, R = 0.2199 (Rfree = 0.000) for 6661 atoms. Found 15 (42 requested) and removed 35 (21 requested) atoms. Cycle 25: After refmac, R = 0.2167 (Rfree = 0.000) for 6618 atoms. Found 16 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 2.76 Search for helices and strands: 0 residues in 0 chains, 6856 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6881 seeds are put forward Round 1: 487 peptides, 73 chains. Longest chain 18 peptides. Score 0.419 Round 2: 525 peptides, 64 chains. Longest chain 22 peptides. Score 0.502 Round 3: 537 peptides, 64 chains. Longest chain 30 peptides. Score 0.513 Round 4: 528 peptides, 60 chains. Longest chain 27 peptides. Score 0.523 Round 5: 542 peptides, 65 chains. Longest chain 20 peptides. Score 0.514 Taking the results from Round 4 Chains 62, Residues 468, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14953 restraints for refining 6788 atoms. 12971 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2500 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 50 (21 requested) atoms. Cycle 27: After refmac, R = 0.2377 (Rfree = 0.000) for 6753 atoms. Found 35 (43 requested) and removed 36 (21 requested) atoms. Cycle 28: After refmac, R = 0.2291 (Rfree = 0.000) for 6742 atoms. Found 16 (43 requested) and removed 36 (21 requested) atoms. Cycle 29: After refmac, R = 0.2202 (Rfree = 0.000) for 6711 atoms. Found 11 (43 requested) and removed 24 (21 requested) atoms. Cycle 30: After refmac, R = 0.2161 (Rfree = 0.000) for 6689 atoms. Found 9 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.78 Search for helices and strands: 0 residues in 0 chains, 6937 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6960 seeds are put forward Round 1: 516 peptides, 72 chains. Longest chain 33 peptides. Score 0.455 Round 2: 539 peptides, 67 chains. Longest chain 22 peptides. Score 0.502 Round 3: 537 peptides, 68 chains. Longest chain 22 peptides. Score 0.495 Round 4: 563 peptides, 64 chains. Longest chain 36 peptides. Score 0.538 Round 5: 550 peptides, 62 chains. Longest chain 30 peptides. Score 0.535 Taking the results from Round 4 Chains 70, Residues 499, Estimated correctness of the model 0.0 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14571 restraints for refining 6788 atoms. 12444 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2537 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 35 (21 requested) atoms. Cycle 32: After refmac, R = 0.2374 (Rfree = 0.000) for 6756 atoms. Found 27 (43 requested) and removed 31 (21 requested) atoms. Cycle 33: After refmac, R = 0.2365 (Rfree = 0.000) for 6731 atoms. Found 29 (43 requested) and removed 26 (21 requested) atoms. Cycle 34: After refmac, R = 0.2345 (Rfree = 0.000) for 6717 atoms. Found 21 (43 requested) and removed 28 (21 requested) atoms. Cycle 35: After refmac, R = 0.2281 (Rfree = 0.000) for 6694 atoms. Found 17 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 2.80 Search for helices and strands: 0 residues in 0 chains, 6965 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6986 seeds are put forward Round 1: 472 peptides, 68 chains. Longest chain 21 peptides. Score 0.427 Round 2: 511 peptides, 67 chains. Longest chain 35 peptides. Score 0.473 Round 3: 505 peptides, 63 chains. Longest chain 25 peptides. Score 0.486 Round 4: 517 peptides, 60 chains. Longest chain 31 peptides. Score 0.512 Round 5: 521 peptides, 68 chains. Longest chain 23 peptides. Score 0.479 Taking the results from Round 4 Chains 64, Residues 457, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 17421 reflections ( 99.85 % complete ) and 15139 restraints for refining 6788 atoms. 13249 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2559 (Rfree = 0.000) for 6788 atoms. Found 43 (43 requested) and removed 36 (21 requested) atoms. Cycle 37: After refmac, R = 0.2403 (Rfree = 0.000) for 6748 atoms. Found 26 (43 requested) and removed 33 (21 requested) atoms. Cycle 38: After refmac, R = 0.2339 (Rfree = 0.000) for 6734 atoms. Found 16 (43 requested) and removed 25 (21 requested) atoms. Cycle 39: After refmac, R = 0.2292 (Rfree = 0.000) for 6713 atoms. Found 19 (43 requested) and removed 25 (21 requested) atoms. Cycle 40: After refmac, R = 0.2259 (Rfree = 0.000) for 6698 atoms. Found 16 (43 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.79 Search for helices and strands: 0 residues in 0 chains, 6975 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 6992 seeds are put forward Round 1: 467 peptides, 76 chains. Longest chain 17 peptides. Score 0.381 Round 2: 503 peptides, 63 chains. Longest chain 23 peptides. Score 0.484 Round 3: 499 peptides, 62 chains. Longest chain 22 peptides. Score 0.485 Round 4: 534 peptides, 60 chains. Longest chain 30 peptides. Score 0.529 Round 5: 521 peptides, 63 chains. Longest chain 23 peptides. Score 0.502 Taking the results from Round 4 Chains 61, Residues 474, Estimated correctness of the model 0.0 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 17421 reflections ( 99.85 % complete ) and 14557 restraints for refining 6786 atoms. 12417 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2514 (Rfree = 0.000) for 6786 atoms. Found 43 (43 requested) and removed 50 (21 requested) atoms. Cycle 42: After refmac, R = 0.2411 (Rfree = 0.000) for 6725 atoms. Found 30 (43 requested) and removed 34 (21 requested) atoms. Cycle 43: After refmac, R = 0.2281 (Rfree = 0.000) for 6697 atoms. Found 20 (43 requested) and removed 31 (21 requested) atoms. Cycle 44: After refmac, R = 0.2223 (Rfree = 0.000) for 6667 atoms. Found 17 (42 requested) and removed 25 (21 requested) atoms. Cycle 45: After refmac, R = 0.2187 (Rfree = 0.000) for 6646 atoms. Found 18 (42 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 2.74 Search for helices and strands: 0 residues in 0 chains, 6882 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6904 seeds are put forward Round 1: 450 peptides, 71 chains. Longest chain 22 peptides. Score 0.387 Round 2: 502 peptides, 64 chains. Longest chain 42 peptides. Score 0.478 Round 3: 512 peptides, 65 chains. Longest chain 29 peptides. Score 0.484 Round 4: 503 peptides, 65 chains. Longest chain 30 peptides. Score 0.475 Round 5: 510 peptides, 69 chains. Longest chain 22 peptides. Score 0.463 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 447, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 17421 reflections ( 99.85 % complete ) and 15201 restraints for refining 6787 atoms. 13379 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2470 (Rfree = 0.000) for 6787 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2397 (Rfree = 0.000) for 6730 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2364 (Rfree = 0.000) for 6693 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2343 (Rfree = 0.000) for 6663 atoms. TimeTaking 83.55