Mon 24 Dec 00:51:38 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 1vm8-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vm8-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.6-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/1vm8-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.6-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 00:51:43 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/1vm8-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vm8-3.6-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 818 and 0 Target number of residues in the AU: 818 Target solvent content: 0.6433 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-3.6-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: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.60 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: 105.560 3.600 Wilson plot Bfac: 73.86 14307 reflections ( 99.11 % complete ) and 0 restraints for refining 9454 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2870 (Rfree = 0.000) for 9454 atoms. Found 60 (60 requested) and removed 93 (30 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 9588 seeds are put forward NCS extension: 0 residues added, 9588 seeds are put forward Round 1: 458 peptides, 90 chains. Longest chain 13 peptides. Score 0.314 Round 2: 540 peptides, 80 chains. Longest chain 14 peptides. Score 0.477 Round 3: 577 peptides, 72 chains. Longest chain 21 peptides. Score 0.559 Round 4: 577 peptides, 76 chains. Longest chain 22 peptides. Score 0.539 Round 5: 583 peptides, 71 chains. Longest chain 33 peptides. Score 0.570 Taking the results from Round 5 Chains 76, Residues 512, Estimated correctness of the model 2.6 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17613 restraints for refining 7742 atoms. 15466 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2338 (Rfree = 0.000) for 7742 atoms. Found 39 (49 requested) and removed 59 (24 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2120 (Rfree = 0.000) for 7610 atoms. Found 16 (49 requested) and removed 47 (24 requested) atoms. Cycle 3: After refmac, R = 0.2042 (Rfree = 0.000) for 7537 atoms. Found 14 (48 requested) and removed 31 (24 requested) atoms. Cycle 4: After refmac, R = 0.1978 (Rfree = 0.000) for 7504 atoms. Found 14 (48 requested) and removed 28 (24 requested) atoms. Cycle 5: After refmac, R = 0.1935 (Rfree = 0.000) for 7473 atoms. Found 13 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 7720 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7735 seeds are put forward Round 1: 516 peptides, 79 chains. Longest chain 24 peptides. Score 0.454 Round 2: 610 peptides, 81 chains. Longest chain 27 peptides. Score 0.551 Round 3: 594 peptides, 72 chains. Longest chain 25 peptides. Score 0.576 Round 4: 595 peptides, 71 chains. Longest chain 35 peptides. Score 0.582 Round 5: 612 peptides, 81 chains. Longest chain 28 peptides. Score 0.553 Taking the results from Round 4 Chains 71, Residues 524, Estimated correctness of the model 7.5 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17702 restraints for refining 7743 atoms. 15527 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2237 (Rfree = 0.000) for 7743 atoms. Found 37 (49 requested) and removed 61 (24 requested) atoms. Cycle 7: After refmac, R = 0.2009 (Rfree = 0.000) for 7682 atoms. Found 14 (49 requested) and removed 46 (24 requested) atoms. Cycle 8: After refmac, R = 0.1964 (Rfree = 0.000) for 7631 atoms. Found 13 (49 requested) and removed 42 (24 requested) atoms. Cycle 9: After refmac, R = 0.1984 (Rfree = 0.000) for 7594 atoms. Found 17 (48 requested) and removed 37 (24 requested) atoms. Cycle 10: After refmac, R = 0.1927 (Rfree = 0.000) for 7561 atoms. Found 21 (48 requested) and removed 45 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 7782 seeds are put forward NCS extension: 50 residues added (2 deleted due to clashes), 7832 seeds are put forward Round 1: 523 peptides, 87 chains. Longest chain 23 peptides. Score 0.419 Round 2: 553 peptides, 78 chains. Longest chain 26 peptides. Score 0.503 Round 3: 566 peptides, 83 chains. Longest chain 24 peptides. Score 0.492 Round 4: 578 peptides, 77 chains. Longest chain 37 peptides. Score 0.536 Round 5: 575 peptides, 74 chains. Longest chain 32 peptides. Score 0.547 Taking the results from Round 5 Chains 78, Residues 501, Estimated correctness of the model 0.0 % 8 chains (80 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17148 restraints for refining 7745 atoms. 14936 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2226 (Rfree = 0.000) for 7745 atoms. Found 44 (49 requested) and removed 63 (24 requested) atoms. Cycle 12: After refmac, R = 0.2083 (Rfree = 0.000) for 7686 atoms. Found 30 (49 requested) and removed 41 (24 requested) atoms. Cycle 13: After refmac, R = 0.1965 (Rfree = 0.000) for 7646 atoms. Found 32 (49 requested) and removed 35 (24 requested) atoms. Cycle 14: After refmac, R = 0.1917 (Rfree = 0.000) for 7621 atoms. Found 25 (49 requested) and removed 40 (24 requested) atoms. Cycle 15: After refmac, R = 0.1857 (Rfree = 0.000) for 7592 atoms. Found 30 (48 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7836 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7860 seeds are put forward Round 1: 474 peptides, 80 chains. Longest chain 15 peptides. Score 0.395 Round 2: 523 peptides, 73 chains. Longest chain 34 peptides. Score 0.494 Round 3: 545 peptides, 81 chains. Longest chain 23 peptides. Score 0.478 Round 4: 550 peptides, 74 chains. Longest chain 43 peptides. Score 0.519 Round 5: 545 peptides, 74 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 4 Chains 81, Residues 476, Estimated correctness of the model 0.0 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17262 restraints for refining 7744 atoms. 15163 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2053 (Rfree = 0.000) for 7744 atoms. Found 40 (49 requested) and removed 61 (24 requested) atoms. Cycle 17: After refmac, R = 0.1929 (Rfree = 0.000) for 7675 atoms. Found 17 (49 requested) and removed 35 (24 requested) atoms. Cycle 18: After refmac, R = 0.1885 (Rfree = 0.000) for 7624 atoms. Found 20 (49 requested) and removed 36 (24 requested) atoms. Cycle 19: After refmac, R = 0.1809 (Rfree = 0.000) for 7591 atoms. Found 17 (48 requested) and removed 56 (24 requested) atoms. Cycle 20: After refmac, R = 0.1750 (Rfree = 0.000) for 7537 atoms. Found 8 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7732 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7751 seeds are put forward Round 1: 490 peptides, 86 chains. Longest chain 15 peptides. Score 0.382 Round 2: 525 peptides, 76 chains. Longest chain 16 peptides. Score 0.480 Round 3: 554 peptides, 78 chains. Longest chain 19 peptides. Score 0.504 Round 4: 523 peptides, 72 chains. Longest chain 19 peptides. Score 0.499 Round 5: 520 peptides, 73 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 3 Chains 79, Residues 476, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17423 restraints for refining 7743 atoms. 15493 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2029 (Rfree = 0.000) for 7743 atoms. Found 32 (49 requested) and removed 46 (24 requested) atoms. Cycle 22: After refmac, R = 0.1935 (Rfree = 0.000) for 7695 atoms. Found 14 (49 requested) and removed 41 (24 requested) atoms. Cycle 23: After refmac, R = 0.1987 (Rfree = 0.000) for 7657 atoms. Found 20 (49 requested) and removed 37 (24 requested) atoms. Cycle 24: After refmac, R = 0.1853 (Rfree = 0.000) for 7629 atoms. Found 19 (49 requested) and removed 32 (24 requested) atoms. Cycle 25: After refmac, R = 0.1870 (Rfree = 0.000) for 7606 atoms. Found 19 (48 requested) and removed 35 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 7818 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7831 seeds are put forward Round 1: 485 peptides, 89 chains. Longest chain 16 peptides. Score 0.358 Round 2: 525 peptides, 82 chains. Longest chain 19 peptides. Score 0.448 Round 3: 515 peptides, 78 chains. Longest chain 21 peptides. Score 0.458 Round 4: 528 peptides, 77 chains. Longest chain 17 peptides. Score 0.479 Round 5: 500 peptides, 76 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 4 Chains 78, Residues 451, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17518 restraints for refining 7743 atoms. 15669 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2166 (Rfree = 0.000) for 7743 atoms. Found 32 (49 requested) and removed 47 (24 requested) atoms. Cycle 27: After refmac, R = 0.1960 (Rfree = 0.000) for 7691 atoms. Found 28 (49 requested) and removed 31 (24 requested) atoms. Cycle 28: After refmac, R = 0.1896 (Rfree = 0.000) for 7668 atoms. Found 25 (49 requested) and removed 33 (24 requested) atoms. Cycle 29: After refmac, R = 0.1838 (Rfree = 0.000) for 7645 atoms. Found 27 (49 requested) and removed 32 (24 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1815 (Rfree = 0.000) for 7629 atoms. Found 21 (49 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 7847 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 7871 seeds are put forward Round 1: 421 peptides, 79 chains. Longest chain 19 peptides. Score 0.328 Round 2: 478 peptides, 81 chains. Longest chain 18 peptides. Score 0.394 Round 3: 484 peptides, 79 chains. Longest chain 19 peptides. Score 0.413 Round 4: 496 peptides, 76 chains. Longest chain 21 peptides. Score 0.445 Round 5: 510 peptides, 76 chains. Longest chain 25 peptides. Score 0.462 Taking the results from Round 5 Chains 78, Residues 434, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 18088 restraints for refining 7744 atoms. 16375 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2121 (Rfree = 0.000) for 7744 atoms. Found 36 (49 requested) and removed 33 (24 requested) atoms. Cycle 32: After refmac, R = 0.1930 (Rfree = 0.000) for 7721 atoms. Found 14 (49 requested) and removed 32 (24 requested) atoms. Cycle 33: After refmac, R = 0.1886 (Rfree = 0.000) for 7694 atoms. Found 24 (49 requested) and removed 31 (24 requested) atoms. Cycle 34: After refmac, R = 0.1834 (Rfree = 0.000) for 7666 atoms. Found 15 (49 requested) and removed 29 (24 requested) atoms. Cycle 35: After refmac, R = 0.1773 (Rfree = 0.000) for 7644 atoms. Found 19 (49 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 7860 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 7878 seeds are put forward Round 1: 404 peptides, 76 chains. Longest chain 17 peptides. Score 0.322 Round 2: 486 peptides, 75 chains. Longest chain 20 peptides. Score 0.438 Round 3: 486 peptides, 74 chains. Longest chain 17 peptides. Score 0.444 Round 4: 483 peptides, 79 chains. Longest chain 15 peptides. Score 0.412 Round 5: 483 peptides, 74 chains. Longest chain 16 peptides. Score 0.440 Taking the results from Round 3 Chains 74, Residues 412, Estimated correctness of the model 0.0 % 7 chains (34 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17724 restraints for refining 7744 atoms. 16051 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2093 (Rfree = 0.000) for 7744 atoms. Found 26 (49 requested) and removed 32 (24 requested) atoms. Cycle 37: After refmac, R = 0.2023 (Rfree = 0.000) for 7711 atoms. Found 37 (49 requested) and removed 39 (24 requested) atoms. Cycle 38: After refmac, R = 0.1894 (Rfree = 0.000) for 7692 atoms. Found 24 (49 requested) and removed 29 (24 requested) atoms. Cycle 39: After refmac, R = 0.1828 (Rfree = 0.000) for 7672 atoms. Found 20 (49 requested) and removed 27 (24 requested) atoms. Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 7657 atoms. Found 25 (49 requested) and removed 30 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 7894 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7908 seeds are put forward Round 1: 403 peptides, 78 chains. Longest chain 12 peptides. Score 0.309 Round 2: 443 peptides, 75 chains. Longest chain 19 peptides. Score 0.382 Round 3: 438 peptides, 70 chains. Longest chain 20 peptides. Score 0.405 Round 4: 454 peptides, 71 chains. Longest chain 21 peptides. Score 0.420 Round 5: 425 peptides, 67 chains. Longest chain 21 peptides. Score 0.405 Taking the results from Round 4 Chains 71, Residues 383, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17992 restraints for refining 7743 atoms. 16472 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1846 (Rfree = 0.000) for 7743 atoms. Found 25 (49 requested) and removed 30 (24 requested) atoms. Cycle 42: After refmac, R = 0.1877 (Rfree = 0.000) for 7718 atoms. Found 27 (49 requested) and removed 31 (24 requested) atoms. Cycle 43: After refmac, R = 0.1774 (Rfree = 0.000) for 7703 atoms. Found 26 (49 requested) and removed 29 (24 requested) atoms. Cycle 44: After refmac, R = 0.1828 (Rfree = 0.000) for 7691 atoms. Found 42 (49 requested) and removed 33 (24 requested) atoms. Cycle 45: After refmac, R = 0.1732 (Rfree = 0.000) for 7693 atoms. Found 24 (49 requested) and removed 35 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 7923 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 7948 seeds are put forward Round 1: 381 peptides, 77 chains. Longest chain 11 peptides. Score 0.282 Round 2: 423 peptides, 67 chains. Longest chain 23 peptides. Score 0.403 Round 3: 430 peptides, 64 chains. Longest chain 24 peptides. Score 0.429 Round 4: 421 peptides, 67 chains. Longest chain 17 peptides. Score 0.400 Round 5: 418 peptides, 65 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 366, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (366 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14307 reflections ( 99.11 % complete ) and 18100 restraints for refining 7742 atoms. 16622 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1886 (Rfree = 0.000) for 7742 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1828 (Rfree = 0.000) for 7699 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1802 (Rfree = 0.000) for 7664 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.1732 (Rfree = 0.000) for 7634 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Writing output files ... TimeTaking 87.88