Mon 24 Dec 00:20:50 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl5-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-mrncs ############### 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 00:20:54 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-mrncs/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 783 and 0 Target number of residues in the AU: 783 Target solvent content: 0.6342 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: 1vl5-3.6-parrot-mrncs.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: 1vl5-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 68.61 13375 reflections ( 99.90 % complete ) and 0 restraints for refining 9208 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3135 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2898 (Rfree = 0.000) for 9208 atoms. Found 59 (59 requested) and removed 56 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 9339 seeds are put forward NCS extension: 0 residues added, 9339 seeds are put forward Round 1: 400 peptides, 71 chains. Longest chain 13 peptides. Score 0.356 Round 2: 519 peptides, 81 chains. Longest chain 15 peptides. Score 0.461 Round 3: 557 peptides, 78 chains. Longest chain 19 peptides. Score 0.524 Round 4: 572 peptides, 76 chains. Longest chain 23 peptides. Score 0.552 Round 5: 590 peptides, 78 chains. Longest chain 33 peptides. Score 0.562 Taking the results from Round 5 Chains 81, Residues 512, Estimated correctness of the model 0.0 % 6 chains (57 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16820 restraints for refining 7536 atoms. 14660 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2269 (Rfree = 0.000) for 7536 atoms. Found 29 (48 requested) and removed 58 (24 requested) atoms. Cycle 2: After refmac, R = 0.2077 (Rfree = 0.000) for 7385 atoms. Found 23 (48 requested) and removed 39 (24 requested) atoms. Cycle 3: After refmac, R = 0.1974 (Rfree = 0.000) for 7321 atoms. Found 16 (47 requested) and removed 31 (23 requested) atoms. Cycle 4: After refmac, R = 0.1955 (Rfree = 0.000) for 7266 atoms. Found 19 (46 requested) and removed 32 (23 requested) atoms. Cycle 5: After refmac, R = 0.1739 (Rfree = 0.000) for 7227 atoms. Found 22 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 7482 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 7509 seeds are put forward Round 1: 516 peptides, 80 chains. Longest chain 17 peptides. Score 0.462 Round 2: 573 peptides, 79 chains. Longest chain 18 peptides. Score 0.537 Round 3: 591 peptides, 75 chains. Longest chain 26 peptides. Score 0.578 Round 4: 608 peptides, 82 chains. Longest chain 20 peptides. Score 0.562 Round 5: 594 peptides, 70 chains. Longest chain 25 peptides. Score 0.605 Taking the results from Round 5 Chains 72, Residues 524, Estimated correctness of the model 16.6 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16796 restraints for refining 7506 atoms. 14660 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2320 (Rfree = 0.000) for 7506 atoms. Found 30 (48 requested) and removed 90 (24 requested) atoms. Cycle 7: After refmac, R = 0.2083 (Rfree = 0.000) for 7380 atoms. Found 22 (47 requested) and removed 49 (23 requested) atoms. Cycle 8: After refmac, R = 0.1961 (Rfree = 0.000) for 7317 atoms. Found 33 (47 requested) and removed 41 (23 requested) atoms. Cycle 9: After refmac, R = 0.1795 (Rfree = 0.000) for 7283 atoms. Found 16 (46 requested) and removed 37 (23 requested) atoms. Cycle 10: After refmac, R = 0.1779 (Rfree = 0.000) for 7243 atoms. Found 19 (46 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 7445 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7470 seeds are put forward Round 1: 518 peptides, 83 chains. Longest chain 16 peptides. Score 0.448 Round 2: 570 peptides, 82 chains. Longest chain 24 peptides. Score 0.518 Round 3: 587 peptides, 78 chains. Longest chain 16 peptides. Score 0.558 Round 4: 601 peptides, 74 chains. Longest chain 24 peptides. Score 0.593 Round 5: 576 peptides, 75 chains. Longest chain 20 peptides. Score 0.561 Taking the results from Round 4 Chains 77, Residues 527, Estimated correctness of the model 11.9 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16684 restraints for refining 7540 atoms. 14491 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2085 (Rfree = 0.000) for 7540 atoms. Found 27 (48 requested) and removed 55 (24 requested) atoms. Cycle 12: After refmac, R = 0.1970 (Rfree = 0.000) for 7477 atoms. Found 30 (48 requested) and removed 40 (24 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1883 (Rfree = 0.000) for 7452 atoms. Found 11 (47 requested) and removed 29 (23 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1835 (Rfree = 0.000) for 7413 atoms. Found 10 (47 requested) and removed 28 (23 requested) atoms. Cycle 15: After refmac, R = 0.1819 (Rfree = 0.000) for 7381 atoms. Found 11 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7636 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 7655 seeds are put forward Round 1: 468 peptides, 80 chains. Longest chain 15 peptides. Score 0.398 Round 2: 555 peptides, 81 chains. Longest chain 20 peptides. Score 0.506 Round 3: 547 peptides, 80 chains. Longest chain 17 peptides. Score 0.501 Round 4: 551 peptides, 73 chains. Longest chain 18 peptides. Score 0.543 Round 5: 565 peptides, 69 chains. Longest chain 18 peptides. Score 0.579 Taking the results from Round 5 Chains 70, Residues 496, Estimated correctness of the model 6.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17206 restraints for refining 7541 atoms. 15252 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2209 (Rfree = 0.000) for 7541 atoms. Found 32 (48 requested) and removed 35 (24 requested) atoms. Cycle 17: After refmac, R = 0.2044 (Rfree = 0.000) for 7497 atoms. Found 24 (48 requested) and removed 46 (24 requested) atoms. Cycle 18: After refmac, R = 0.1959 (Rfree = 0.000) for 7450 atoms. Found 25 (47 requested) and removed 35 (23 requested) atoms. Cycle 19: After refmac, R = 0.1896 (Rfree = 0.000) for 7420 atoms. Found 26 (47 requested) and removed 30 (23 requested) atoms. Cycle 20: After refmac, R = 0.1852 (Rfree = 0.000) for 7407 atoms. Found 22 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 7656 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7679 seeds are put forward Round 1: 498 peptides, 88 chains. Longest chain 13 peptides. Score 0.392 Round 2: 545 peptides, 79 chains. Longest chain 24 peptides. Score 0.504 Round 3: 558 peptides, 78 chains. Longest chain 17 peptides. Score 0.525 Round 4: 532 peptides, 77 chains. Longest chain 19 peptides. Score 0.499 Round 5: 534 peptides, 73 chains. Longest chain 19 peptides. Score 0.523 Taking the results from Round 3 Chains 79, Residues 480, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16892 restraints for refining 7542 atoms. 14933 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2045 (Rfree = 0.000) for 7542 atoms. Found 30 (48 requested) and removed 46 (24 requested) atoms. Cycle 22: After refmac, R = 0.1961 (Rfree = 0.000) for 7495 atoms. Found 26 (48 requested) and removed 37 (24 requested) atoms. Cycle 23: After refmac, R = 0.1860 (Rfree = 0.000) for 7473 atoms. Found 17 (48 requested) and removed 33 (24 requested) atoms. Cycle 24: After refmac, R = 0.1770 (Rfree = 0.000) for 7441 atoms. Found 11 (47 requested) and removed 27 (23 requested) atoms. Cycle 25: After refmac, R = 0.1718 (Rfree = 0.000) for 7412 atoms. Found 17 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7628 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7647 seeds are put forward Round 1: 479 peptides, 82 chains. Longest chain 14 peptides. Score 0.401 Round 2: 516 peptides, 76 chains. Longest chain 16 peptides. Score 0.485 Round 3: 540 peptides, 80 chains. Longest chain 15 peptides. Score 0.493 Round 4: 542 peptides, 78 chains. Longest chain 24 peptides. Score 0.506 Round 5: 546 peptides, 75 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 5 Chains 79, Residues 471, Estimated correctness of the model 0.0 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16971 restraints for refining 7539 atoms. 15021 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2059 (Rfree = 0.000) for 7539 atoms. Found 36 (48 requested) and removed 38 (24 requested) atoms. Cycle 27: After refmac, R = 0.1923 (Rfree = 0.000) for 7506 atoms. Found 20 (48 requested) and removed 34 (24 requested) atoms. Cycle 28: After refmac, R = 0.1810 (Rfree = 0.000) for 7472 atoms. Found 21 (48 requested) and removed 32 (24 requested) atoms. Cycle 29: After refmac, R = 0.1835 (Rfree = 0.000) for 7448 atoms. Found 27 (47 requested) and removed 37 (23 requested) atoms. Cycle 30: After refmac, R = 0.1688 (Rfree = 0.000) for 7426 atoms. Found 16 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7689 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7702 seeds are put forward Round 1: 460 peptides, 84 chains. Longest chain 13 peptides. Score 0.362 Round 2: 485 peptides, 76 chains. Longest chain 16 peptides. Score 0.445 Round 3: 533 peptides, 84 chains. Longest chain 19 peptides. Score 0.462 Round 4: 525 peptides, 77 chains. Longest chain 28 peptides. Score 0.491 Round 5: 515 peptides, 73 chains. Longest chain 18 peptides. Score 0.500 Taking the results from Round 5 Chains 74, Residues 442, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17286 restraints for refining 7542 atoms. 15464 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2237 (Rfree = 0.000) for 7542 atoms. Found 48 (48 requested) and removed 45 (24 requested) atoms. Cycle 32: After refmac, R = 0.1954 (Rfree = 0.000) for 7499 atoms. Found 25 (48 requested) and removed 32 (24 requested) atoms. Cycle 33: After refmac, R = 0.1856 (Rfree = 0.000) for 7479 atoms. Found 17 (48 requested) and removed 36 (24 requested) atoms. Cycle 34: After refmac, R = 0.1779 (Rfree = 0.000) for 7447 atoms. Found 23 (47 requested) and removed 27 (23 requested) atoms. Cycle 35: After refmac, R = 0.1744 (Rfree = 0.000) for 7430 atoms. Found 19 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7678 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7698 seeds are put forward Round 1: 443 peptides, 87 chains. Longest chain 13 peptides. Score 0.319 Round 2: 475 peptides, 85 chains. Longest chain 17 peptides. Score 0.378 Round 3: 489 peptides, 81 chains. Longest chain 14 peptides. Score 0.421 Round 4: 510 peptides, 81 chains. Longest chain 16 peptides. Score 0.449 Round 5: 508 peptides, 80 chains. Longest chain 18 peptides. Score 0.452 Taking the results from Round 5 Chains 80, Residues 428, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17553 restraints for refining 7542 atoms. 15889 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2203 (Rfree = 0.000) for 7542 atoms. Found 35 (48 requested) and removed 39 (24 requested) atoms. Cycle 37: After refmac, R = 0.2050 (Rfree = 0.000) for 7495 atoms. Found 30 (48 requested) and removed 28 (24 requested) atoms. Cycle 38: After refmac, R = 0.1985 (Rfree = 0.000) for 7477 atoms. Found 25 (48 requested) and removed 32 (24 requested) atoms. Cycle 39: After refmac, R = 0.1919 (Rfree = 0.000) for 7455 atoms. Found 33 (47 requested) and removed 28 (23 requested) atoms. Cycle 40: After refmac, R = 0.1780 (Rfree = 0.000) for 7449 atoms. Found 24 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 7703 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7723 seeds are put forward Round 1: 395 peptides, 81 chains. Longest chain 12 peptides. Score 0.284 Round 2: 449 peptides, 77 chains. Longest chain 19 peptides. Score 0.390 Round 3: 441 peptides, 73 chains. Longest chain 15 peptides. Score 0.403 Round 4: 450 peptides, 75 chains. Longest chain 14 peptides. Score 0.403 Round 5: 453 peptides, 71 chains. Longest chain 19 peptides. Score 0.431 Taking the results from Round 5 Chains 71, Residues 382, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17928 restraints for refining 7542 atoms. 16471 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2107 (Rfree = 0.000) for 7542 atoms. Found 46 (48 requested) and removed 34 (24 requested) atoms. Cycle 42: After refmac, R = 0.1928 (Rfree = 0.000) for 7525 atoms. Found 20 (48 requested) and removed 34 (24 requested) atoms. Cycle 43: After refmac, R = 0.1827 (Rfree = 0.000) for 7488 atoms. Found 18 (48 requested) and removed 31 (24 requested) atoms. Cycle 44: After refmac, R = 0.1764 (Rfree = 0.000) for 7459 atoms. Found 22 (47 requested) and removed 31 (23 requested) atoms. Cycle 45: After refmac, R = 0.1761 (Rfree = 0.000) for 7442 atoms. Found 32 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 7685 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 7714 seeds are put forward Round 1: 363 peptides, 71 chains. Longest chain 14 peptides. Score 0.300 Round 2: 431 peptides, 79 chains. Longest chain 14 peptides. Score 0.351 Round 3: 441 peptides, 79 chains. Longest chain 14 peptides. Score 0.366 Round 4: 439 peptides, 73 chains. Longest chain 14 peptides. Score 0.400 Round 5: 413 peptides, 69 chains. Longest chain 18 peptides. Score 0.388 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 73, Residues 366, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 73 chains (366 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 13375 reflections ( 99.90 % complete ) and 17891 restraints for refining 7542 atoms. 16471 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2006 (Rfree = 0.000) for 7542 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1941 (Rfree = 0.000) for 7483 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1898 (Rfree = 0.000) for 7447 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1820 (Rfree = 0.000) for 7415 atoms. TimeTaking 70.83