Sun 23 Dec 22:22:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl5-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl5-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:50 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-parrot-hancs/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 753 and 0 Target number of residues in the AU: 753 Target solvent content: 0.6482 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: 1vl5-3.8-parrot-hancs.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: 1vl5-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.75 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 3.800 Wilson plot Bfac: 76.86 11385 reflections ( 99.89 % complete ) and 0 restraints for refining 9210 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3222 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2933 (Rfree = 0.000) for 9210 atoms. Found 50 (50 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 9364 seeds are put forward NCS extension: 0 residues added, 9364 seeds are put forward Round 1: 446 peptides, 85 chains. Longest chain 17 peptides. Score 0.336 Round 2: 521 peptides, 72 chains. Longest chain 19 peptides. Score 0.513 Round 3: 580 peptides, 73 chains. Longest chain 20 peptides. Score 0.576 Round 4: 569 peptides, 74 chains. Longest chain 21 peptides. Score 0.558 Round 5: 570 peptides, 66 chains. Longest chain 29 peptides. Score 0.599 Taking the results from Round 5 Chains 66, Residues 504, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17357 restraints for refining 7522 atoms. 15362 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2421 (Rfree = 0.000) for 7522 atoms. Found 28 (41 requested) and removed 47 (20 requested) atoms. Cycle 2: After refmac, R = 0.2286 (Rfree = 0.000) for 7381 atoms. Found 28 (41 requested) and removed 50 (20 requested) atoms. Cycle 3: After refmac, R = 0.2147 (Rfree = 0.000) for 7297 atoms. Found 19 (40 requested) and removed 36 (20 requested) atoms. Cycle 4: After refmac, R = 0.2109 (Rfree = 0.000) for 7233 atoms. Found 17 (40 requested) and removed 37 (20 requested) atoms. Cycle 5: After refmac, R = 0.1810 (Rfree = 0.000) for 7176 atoms. Found 9 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 7394 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 7418 seeds are put forward Round 1: 481 peptides, 83 chains. Longest chain 19 peptides. Score 0.398 Round 2: 560 peptides, 85 chains. Longest chain 19 peptides. Score 0.490 Round 3: 542 peptides, 79 chains. Longest chain 16 peptides. Score 0.501 Round 4: 545 peptides, 72 chains. Longest chain 21 peptides. Score 0.541 Round 5: 565 peptides, 75 chains. Longest chain 19 peptides. Score 0.549 Taking the results from Round 5 Chains 76, Residues 490, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17404 restraints for refining 7523 atoms. 15463 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2216 (Rfree = 0.000) for 7523 atoms. Found 38 (41 requested) and removed 43 (20 requested) atoms. Cycle 7: After refmac, R = 0.2088 (Rfree = 0.000) for 7467 atoms. Found 20 (41 requested) and removed 39 (20 requested) atoms. Cycle 8: After refmac, R = 0.2039 (Rfree = 0.000) for 7406 atoms. Found 18 (40 requested) and removed 40 (20 requested) atoms. Cycle 9: After refmac, R = 0.1910 (Rfree = 0.000) for 7361 atoms. Found 17 (40 requested) and removed 41 (20 requested) atoms. Cycle 10: After refmac, R = 0.1851 (Rfree = 0.000) for 7318 atoms. Found 9 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 7526 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 7550 seeds are put forward Round 1: 488 peptides, 84 chains. Longest chain 14 peptides. Score 0.402 Round 2: 524 peptides, 74 chains. Longest chain 22 peptides. Score 0.506 Round 3: 548 peptides, 80 chains. Longest chain 16 peptides. Score 0.503 Round 4: 520 peptides, 75 chains. Longest chain 22 peptides. Score 0.495 Round 5: 529 peptides, 79 chains. Longest chain 15 peptides. Score 0.484 Taking the results from Round 2 Chains 76, Residues 450, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17297 restraints for refining 7475 atoms. 15525 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1941 (Rfree = 0.000) for 7475 atoms. Found 28 (41 requested) and removed 62 (20 requested) atoms. Cycle 12: After refmac, R = 0.1842 (Rfree = 0.000) for 7399 atoms. Found 18 (40 requested) and removed 36 (20 requested) atoms. Cycle 13: After refmac, R = 0.1767 (Rfree = 0.000) for 7350 atoms. Found 14 (40 requested) and removed 35 (20 requested) atoms. Cycle 14: After refmac, R = 0.1749 (Rfree = 0.000) for 7313 atoms. Found 19 (40 requested) and removed 34 (20 requested) atoms. Cycle 15: After refmac, R = 0.1708 (Rfree = 0.000) for 7281 atoms. Found 19 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 7563 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7583 seeds are put forward Round 1: 465 peptides, 84 chains. Longest chain 14 peptides. Score 0.370 Round 2: 501 peptides, 79 chains. Longest chain 14 peptides. Score 0.449 Round 3: 507 peptides, 77 chains. Longest chain 19 peptides. Score 0.468 Round 4: 505 peptides, 70 chains. Longest chain 19 peptides. Score 0.504 Round 5: 506 peptides, 72 chains. Longest chain 26 peptides. Score 0.495 Taking the results from Round 4 Chains 70, Residues 435, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11385 reflections ( 99.89 % complete ) and 17528 restraints for refining 7524 atoms. 15858 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1972 (Rfree = 0.000) for 7524 atoms. Found 19 (41 requested) and removed 55 (20 requested) atoms. Cycle 17: After refmac, R = 0.1972 (Rfree = 0.000) for 7438 atoms. Found 31 (41 requested) and removed 37 (20 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1926 (Rfree = 0.000) for 7406 atoms. Found 34 (40 requested) and removed 38 (20 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1928 (Rfree = 0.000) for 7381 atoms. Found 35 (40 requested) and removed 37 (20 requested) atoms. Cycle 20: After refmac, R = 0.1875 (Rfree = 0.000) for 7362 atoms. Found 36 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 7630 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 7657 seeds are put forward Round 1: 436 peptides, 79 chains. Longest chain 13 peptides. Score 0.359 Round 2: 489 peptides, 77 chains. Longest chain 23 peptides. Score 0.444 Round 3: 489 peptides, 71 chains. Longest chain 21 peptides. Score 0.479 Round 4: 504 peptides, 70 chains. Longest chain 25 peptides. Score 0.503 Round 5: 523 peptides, 76 chains. Longest chain 26 peptides. Score 0.494 Taking the results from Round 4 Chains 70, Residues 434, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17350 restraints for refining 7525 atoms. 15657 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2187 (Rfree = 0.000) for 7525 atoms. Found 41 (41 requested) and removed 42 (20 requested) atoms. Cycle 22: After refmac, R = 0.2084 (Rfree = 0.000) for 7461 atoms. Found 41 (41 requested) and removed 53 (20 requested) atoms. Cycle 23: After refmac, R = 0.1982 (Rfree = 0.000) for 7402 atoms. Found 37 (40 requested) and removed 45 (20 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2019 (Rfree = 0.000) for 7371 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 25: After refmac, R = 0.1936 (Rfree = 0.000) for 7357 atoms. Found 40 (40 requested) and removed 34 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.45 Search for helices and strands: 0 residues in 0 chains, 7620 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 7649 seeds are put forward Round 1: 393 peptides, 78 chains. Longest chain 17 peptides. Score 0.301 Round 2: 456 peptides, 73 chains. Longest chain 18 peptides. Score 0.424 Round 3: 472 peptides, 75 chains. Longest chain 17 peptides. Score 0.433 Round 4: 493 peptides, 71 chains. Longest chain 17 peptides. Score 0.484 Round 5: 487 peptides, 68 chains. Longest chain 21 peptides. Score 0.493 Taking the results from Round 5 Chains 68, Residues 419, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17288 restraints for refining 7525 atoms. 15582 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2174 (Rfree = 0.000) for 7525 atoms. Found 41 (41 requested) and removed 49 (20 requested) atoms. Cycle 27: After refmac, R = 0.2032 (Rfree = 0.000) for 7463 atoms. Found 34 (41 requested) and removed 35 (20 requested) atoms. Cycle 28: After refmac, R = 0.1975 (Rfree = 0.000) for 7443 atoms. Found 31 (41 requested) and removed 36 (20 requested) atoms. Cycle 29: After refmac, R = 0.1849 (Rfree = 0.000) for 7422 atoms. Found 32 (40 requested) and removed 33 (20 requested) atoms. Cycle 30: After refmac, R = 0.1547 (Rfree = 0.000) for 7410 atoms. Found 9 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 7654 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 7688 seeds are put forward Round 1: 394 peptides, 79 chains. Longest chain 13 peptides. Score 0.296 Round 2: 442 peptides, 78 chains. Longest chain 15 peptides. Score 0.374 Round 3: 465 peptides, 75 chains. Longest chain 15 peptides. Score 0.424 Round 4: 465 peptides, 70 chains. Longest chain 19 peptides. Score 0.453 Round 5: 493 peptides, 78 chains. Longest chain 22 peptides. Score 0.444 Taking the results from Round 4 Chains 70, Residues 395, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17561 restraints for refining 7524 atoms. 16000 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1968 (Rfree = 0.000) for 7524 atoms. Found 36 (41 requested) and removed 30 (20 requested) atoms. Cycle 32: After refmac, R = 0.1886 (Rfree = 0.000) for 7491 atoms. Found 19 (41 requested) and removed 31 (20 requested) atoms. Cycle 33: After refmac, R = 0.1804 (Rfree = 0.000) for 7469 atoms. Found 15 (41 requested) and removed 31 (20 requested) atoms. Cycle 34: After refmac, R = 0.1764 (Rfree = 0.000) for 7448 atoms. Found 15 (40 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.1764 (Rfree = 0.000) for 7425 atoms. Found 24 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 7660 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 7680 seeds are put forward Round 1: 385 peptides, 74 chains. Longest chain 14 peptides. Score 0.314 Round 2: 431 peptides, 72 chains. Longest chain 12 peptides. Score 0.395 Round 3: 452 peptides, 76 chains. Longest chain 12 peptides. Score 0.400 Round 4: 448 peptides, 71 chains. Longest chain 14 peptides. Score 0.425 Round 5: 438 peptides, 69 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 4 Chains 71, Residues 377, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17704 restraints for refining 7525 atoms. 16227 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1950 (Rfree = 0.000) for 7525 atoms. Found 24 (41 requested) and removed 31 (20 requested) atoms. Cycle 37: After refmac, R = 0.1889 (Rfree = 0.000) for 7492 atoms. Found 20 (41 requested) and removed 33 (20 requested) atoms. Cycle 38: After refmac, R = 0.1803 (Rfree = 0.000) for 7465 atoms. Found 18 (41 requested) and removed 31 (20 requested) atoms. Cycle 39: After refmac, R = 0.1792 (Rfree = 0.000) for 7442 atoms. Found 15 (40 requested) and removed 33 (20 requested) atoms. Cycle 40: After refmac, R = 0.1760 (Rfree = 0.000) for 7421 atoms. Found 25 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 7667 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7683 seeds are put forward Round 1: 371 peptides, 76 chains. Longest chain 11 peptides. Score 0.279 Round 2: 407 peptides, 67 chains. Longest chain 15 peptides. Score 0.392 Round 3: 411 peptides, 67 chains. Longest chain 16 peptides. Score 0.398 Round 4: 414 peptides, 69 chains. Longest chain 11 peptides. Score 0.389 Round 5: 418 peptides, 64 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 5 Chains 64, Residues 354, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17754 restraints for refining 7524 atoms. 16338 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1966 (Rfree = 0.000) for 7524 atoms. Found 28 (41 requested) and removed 33 (20 requested) atoms. Cycle 42: After refmac, R = 0.1808 (Rfree = 0.000) for 7481 atoms. Found 27 (41 requested) and removed 27 (20 requested) atoms. Cycle 43: After refmac, R = 0.1798 (Rfree = 0.000) for 7459 atoms. Found 24 (41 requested) and removed 30 (20 requested) atoms. Cycle 44: After refmac, R = 0.1842 (Rfree = 0.000) for 7432 atoms. Found 29 (40 requested) and removed 28 (20 requested) atoms. Cycle 45: After refmac, R = 0.1856 (Rfree = 0.000) for 7412 atoms. Found 32 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 7631 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7647 seeds are put forward Round 1: 311 peptides, 68 chains. Longest chain 8 peptides. Score 0.236 Round 2: 361 peptides, 69 chains. Longest chain 13 peptides. Score 0.310 Round 3: 389 peptides, 68 chains. Longest chain 15 peptides. Score 0.359 Round 4: 393 peptides, 68 chains. Longest chain 13 peptides. Score 0.365 Round 5: 398 peptides, 68 chains. Longest chain 18 peptides. Score 0.373 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 68, Residues 330, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11385 reflections ( 99.89 % complete ) and 17931 restraints for refining 7502 atoms. 16650 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1845 (Rfree = 0.000) for 7502 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1743 (Rfree = 0.000) for 7450 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1738 (Rfree = 0.000) for 7417 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1735 (Rfree = 0.000) for 7388 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... TimeTaking 92.73