null Mon 24 Dec 00:12:17 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 2nlv-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-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/2nlv-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-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 00:12:22 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/2nlv-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6337 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 224 Adjusted target solvent content: 0.45 Input MTZ file: 2nlv-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: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1792 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: 29.104 3.600 Wilson plot Bfac: 67.84 2645 reflections ( 99.77 % complete ) and 0 restraints for refining 1994 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3468 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3221 (Rfree = 0.000) for 1994 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 2024 seeds are put forward NCS extension: 0 residues added, 2024 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.306 Round 2: 74 peptides, 14 chains. Longest chain 11 peptides. Score 0.323 Round 3: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.345 Round 4: 88 peptides, 17 chains. Longest chain 13 peptides. Score 0.333 Round 5: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 3 Chains 15, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3873 restraints for refining 1623 atoms. 3624 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2701 (Rfree = 0.000) for 1623 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.2436 (Rfree = 0.000) for 1595 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2281 (Rfree = 0.000) for 1586 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2058 (Rfree = 0.000) for 1577 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2064 (Rfree = 0.000) for 1572 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 1620 seeds are put forward NCS extension: 0 residues added, 1620 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 14 peptides. Score 0.331 Round 2: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.358 Round 3: 95 peptides, 15 chains. Longest chain 14 peptides. Score 0.447 Round 4: 96 peptides, 12 chains. Longest chain 15 peptides. Score 0.541 Round 5: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.388 Taking the results from Round 4 Chains 13, Residues 84, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3619 restraints for refining 1617 atoms. 3241 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2465 (Rfree = 0.000) for 1617 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 7: After refmac, R = 0.2207 (Rfree = 0.000) for 1602 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2185 (Rfree = 0.000) for 1599 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2095 (Rfree = 0.000) for 1593 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2088 (Rfree = 0.000) for 1587 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 1631 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1644 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 8 peptides. Score 0.282 Round 2: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.382 Round 3: 104 peptides, 19 chains. Longest chain 13 peptides. Score 0.389 Round 4: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.429 Round 5: 94 peptides, 17 chains. Longest chain 8 peptides. Score 0.378 Taking the results from Round 4 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3828 restraints for refining 1624 atoms. 3509 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2398 (Rfree = 0.000) for 1624 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 12: After refmac, R = 0.2252 (Rfree = 0.000) for 1620 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.2133 (Rfree = 0.000) for 1614 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.2072 (Rfree = 0.000) for 1610 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.1966 (Rfree = 0.000) for 1603 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 1657 seeds are put forward NCS extension: 0 residues added, 1657 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 7 peptides. Score 0.283 Round 2: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.360 Round 3: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.389 Round 4: 109 peptides, 18 chains. Longest chain 10 peptides. Score 0.454 Round 5: 121 peptides, 21 chains. Longest chain 10 peptides. Score 0.448 Taking the results from Round 4 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3751 restraints for refining 1624 atoms. 3405 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2302 (Rfree = 0.000) for 1624 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.2188 (Rfree = 0.000) for 1611 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2067 (Rfree = 0.000) for 1602 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.1879 (Rfree = 0.000) for 1593 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1885 (Rfree = 0.000) for 1589 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 1638 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 1646 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.271 Round 2: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.311 Round 3: 77 peptides, 15 chains. Longest chain 7 peptides. Score 0.313 Round 4: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.390 Round 5: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 4 Chains 15, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3929 restraints for refining 1624 atoms. 3656 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2236 (Rfree = 0.000) for 1624 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2136 (Rfree = 0.000) for 1610 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.1713 (Rfree = 0.000) for 1609 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.1569 (Rfree = 0.000) for 1607 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1646 (Rfree = 0.000) for 1603 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.65 Search for helices and strands: 0 residues in 0 chains, 1638 seeds are put forward NCS extension: 0 residues added, 1638 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.238 Round 2: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.286 Round 3: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.348 Round 4: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.371 Round 5: 91 peptides, 16 chains. Longest chain 8 peptides. Score 0.388 Taking the results from Round 5 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3855 restraints for refining 1623 atoms. 3571 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2033 (Rfree = 0.000) for 1623 atoms. Found 5 (10 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2005 (Rfree = 0.000) for 1613 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.1483 (Rfree = 0.000) for 1611 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.1556 (Rfree = 0.000) for 1604 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.1980 (Rfree = 0.000) for 1595 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 1641 seeds are put forward NCS extension: 0 residues added, 1641 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.303 Round 2: 100 peptides, 18 chains. Longest chain 12 peptides. Score 0.391 Round 3: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.407 Round 4: 95 peptides, 16 chains. Longest chain 13 peptides. Score 0.417 Round 5: 101 peptides, 15 chains. Longest chain 21 peptides. Score 0.488 Taking the results from Round 5 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3669 restraints for refining 1624 atoms. 3340 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1898 (Rfree = 0.000) for 1624 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.1817 (Rfree = 0.000) for 1616 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.1877 (Rfree = 0.000) for 1611 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1811 (Rfree = 0.000) for 1611 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1859 (Rfree = 0.000) for 1609 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 1668 seeds are put forward NCS extension: 0 residues added, 1668 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 8 peptides. Score 0.220 Round 2: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.377 Round 3: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.369 Round 4: 106 peptides, 17 chains. Longest chain 16 peptides. Score 0.463 Round 5: 107 peptides, 15 chains. Longest chain 13 peptides. Score 0.526 Taking the results from Round 5 Chains 15, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3613 restraints for refining 1624 atoms. 3260 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2210 (Rfree = 0.000) for 1624 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.1956 (Rfree = 0.000) for 1611 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1875 (Rfree = 0.000) for 1613 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.1871 (Rfree = 0.000) for 1607 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1782 (Rfree = 0.000) for 1606 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 1643 seeds are put forward NCS extension: 0 residues added, 1643 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.250 Round 2: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.331 Round 3: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.368 Round 4: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.375 Round 5: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 5 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2645 reflections ( 99.77 % complete ) and 3871 restraints for refining 1624 atoms. 3631 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2013 (Rfree = 0.000) for 1624 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.2039 (Rfree = 0.000) for 1617 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.2004 (Rfree = 0.000) for 1616 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1442 (Rfree = 0.000) for 1614 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1275 (Rfree = 0.000) for 1613 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 1650 seeds are put forward NCS extension: 0 residues added, 1650 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.258 Round 2: 76 peptides, 14 chains. Longest chain 11 peptides. Score 0.339 Round 3: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.352 Round 4: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.402 Round 5: 74 peptides, 12 chains. Longest chain 15 peptides. Score 0.391 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nlv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2645 reflections ( 99.77 % complete ) and 3758 restraints for refining 1619 atoms. 3529 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2218 (Rfree = 0.000) for 1619 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2248 (Rfree = 0.000) for 1610 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1997 (Rfree = 0.000) for 1603 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1415 (Rfree = 0.000) for 1598 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:39:16 GMT 2018 Job finished. TimeTaking 26.98 Used memory is bytes: 14975032