null Mon 24 Dec 00:01:23 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.4-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 00:01:27 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.4-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 152 and 0 Target number of residues in the AU: 152 Target solvent content: 0.6263 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 64.64 3120 reflections ( 99.81 % complete ) and 0 restraints for refining 1988 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3450 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3211 (Rfree = 0.000) for 1988 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 0 residues added, 2026 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.289 Round 2: 102 peptides, 18 chains. Longest chain 19 peptides. Score 0.405 Round 3: 101 peptides, 18 chains. Longest chain 11 peptides. Score 0.398 Round 4: 108 peptides, 18 chains. Longest chain 21 peptides. Score 0.447 Round 5: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 4 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3805 restraints for refining 1628 atoms. 3463 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2666 (Rfree = 0.000) for 1628 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2479 (Rfree = 0.000) for 1613 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2252 (Rfree = 0.000) for 1602 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2195 (Rfree = 0.000) for 1596 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2555 (Rfree = 0.000) for 1590 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.41 Search for helices and strands: 0 residues in 0 chains, 1642 seeds are put forward NCS extension: 0 residues added, 1642 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 9 peptides. Score 0.295 Round 2: 117 peptides, 20 chains. Longest chain 16 peptides. Score 0.450 Round 3: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.445 Round 4: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.432 Round 5: 109 peptides, 16 chains. Longest chain 12 peptides. Score 0.511 Taking the results from Round 5 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3780 restraints for refining 1629 atoms. 3424 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2322 (Rfree = 0.000) for 1629 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 7: After refmac, R = 0.2228 (Rfree = 0.000) for 1626 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2374 (Rfree = 0.000) for 1624 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.2042 (Rfree = 0.000) for 1624 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2240 (Rfree = 0.000) for 1618 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.38 Search for helices and strands: 0 residues in 0 chains, 1671 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1684 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 7 peptides. Score 0.284 Round 2: 90 peptides, 14 chains. Longest chain 10 peptides. Score 0.443 Round 3: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.488 Round 4: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.438 Round 5: 102 peptides, 15 chains. Longest chain 10 peptides. Score 0.494 Taking the results from Round 5 Chains 15, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3814 restraints for refining 1629 atoms. 3481 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2506 (Rfree = 0.000) for 1629 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.2192 (Rfree = 0.000) for 1627 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2249 (Rfree = 0.000) for 1620 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2656 (Rfree = 0.000) for 1615 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2589 (Rfree = 0.000) for 1614 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1675 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 1683 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.236 Round 2: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.339 Round 3: 96 peptides, 14 chains. Longest chain 10 peptides. Score 0.484 Round 4: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.434 Round 5: 101 peptides, 17 chains. Longest chain 9 peptides. Score 0.429 Taking the results from Round 3 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3638 restraints for refining 1608 atoms. 3324 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2530 (Rfree = 0.000) for 1608 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2621 (Rfree = 0.000) for 1602 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.2455 (Rfree = 0.000) for 1601 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2332 (Rfree = 0.000) for 1598 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. Cycle 20: After refmac, R = 0.2813 (Rfree = 0.000) for 1588 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 1654 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1663 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.238 Round 2: 87 peptides, 16 chains. Longest chain 12 peptides. Score 0.358 Round 3: 94 peptides, 18 chains. Longest chain 10 peptides. Score 0.347 Round 4: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.331 Round 5: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3676 restraints for refining 1618 atoms. 3384 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2364 (Rfree = 0.000) for 1618 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.2569 (Rfree = 0.000) for 1613 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2550 (Rfree = 0.000) for 1610 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2481 (Rfree = 0.000) for 1610 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 25: After refmac, R = 0.2410 (Rfree = 0.000) for 1608 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 1659 seeds are put forward NCS extension: 0 residues added, 1659 seeds are put forward Round 1: 68 peptides, 16 chains. Longest chain 5 peptides. Score 0.202 Round 2: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.341 Round 3: 83 peptides, 16 chains. Longest chain 12 peptides. Score 0.327 Round 4: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.365 Round 5: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.358 Taking the results from Round 4 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3755 restraints for refining 1629 atoms. 3483 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2405 (Rfree = 0.000) for 1629 atoms. Found 7 (12 requested) and removed 49 (6 requested) atoms. Cycle 27: After refmac, R = 0.2773 (Rfree = 0.000) for 1581 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 28: After refmac, R = 0.2690 (Rfree = 0.000) for 1559 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 29: After refmac, R = 0.2543 (Rfree = 0.000) for 1550 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2481 (Rfree = 0.000) for 1548 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 1578 seeds are put forward NCS extension: 0 residues added, 1578 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.223 Round 2: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 3: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.305 Round 4: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.282 Round 5: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.312 Taking the results from Round 5 Chains 12, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3647 restraints for refining 1589 atoms. 3451 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2634 (Rfree = 0.000) for 1589 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2637 (Rfree = 0.000) for 1582 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2476 (Rfree = 0.000) for 1580 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2495 (Rfree = 0.000) for 1579 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1826 (Rfree = 0.000) for 1582 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 1624 seeds are put forward NCS extension: 0 residues added, 1624 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.222 Round 2: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.279 Round 3: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.347 Round 4: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.313 Round 5: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 3 Chains 14, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3422 restraints for refining 1565 atoms. 3184 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2251 (Rfree = 0.000) for 1565 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.2587 (Rfree = 0.000) for 1560 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2295 (Rfree = 0.000) for 1561 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.2394 (Rfree = 0.000) for 1563 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2257 (Rfree = 0.000) for 1563 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 1596 seeds are put forward NCS extension: 0 residues added, 1596 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.205 Round 2: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.269 Round 3: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.269 Round 4: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.280 Round 5: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.269 Taking the results from Round 4 Chains 11, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3120 reflections ( 99.81 % complete ) and 3663 restraints for refining 1597 atoms. 3494 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2327 (Rfree = 0.000) for 1597 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.2432 (Rfree = 0.000) for 1591 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 1590 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1714 (Rfree = 0.000) for 1589 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1751 (Rfree = 0.000) for 1583 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 1618 seeds are put forward NCS extension: 0 residues added, 1618 seeds are put forward Round 1: 63 peptides, 15 chains. Longest chain 6 peptides. Score 0.194 Round 2: 66 peptides, 14 chains. Longest chain 6 peptides. Score 0.257 Round 3: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.274 Round 4: 69 peptides, 12 chains. Longest chain 13 peptides. Score 0.352 Round 5: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.284 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 57, 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. 3120 reflections ( 99.81 % complete ) and 3695 restraints for refining 1622 atoms. 3479 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2225 (Rfree = 0.000) for 1622 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 1613 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1790 (Rfree = 0.000) for 1606 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1836 (Rfree = 0.000) for 1599 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:21:43 GMT 2018 Job finished. TimeTaking 20.33 Used memory is bytes: 6481536