Mon 24 Dec 07:34:31 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ouw-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-parrot-noncs ############### 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 07:34:36 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/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-parrot-noncs/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 148 and 0 Target number of residues in the AU: 148 Target solvent content: 0.6741 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-4.0-parrot-noncs.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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2208 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: 108.355 4.000 Wilson plot Bfac: 94.17 2488 reflections ( 99.72 % complete ) and 0 restraints for refining 2434 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3957 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3640 (Rfree = 0.000) for 2434 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 4.62 Search for helices and strands: 0 residues in 0 chains, 2499 seeds are put forward NCS extension: 0 residues added, 2499 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.279 Round 2: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.341 Round 3: 100 peptides, 17 chains. Longest chain 9 peptides. Score 0.402 Round 4: 109 peptides, 17 chains. Longest chain 11 peptides. Score 0.458 Round 5: 119 peptides, 17 chains. Longest chain 11 peptides. Score 0.517 Taking the results from Round 5 Chains 17, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 4443 restraints for refining 1887 atoms. 4052 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3117 (Rfree = 0.000) for 1887 atoms. Found 8 (8 requested) and removed 23 (4 requested) atoms. Cycle 2: After refmac, R = 0.3074 (Rfree = 0.000) for 1834 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 3: After refmac, R = 0.3029 (Rfree = 0.000) for 1794 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 4: After refmac, R = 0.3191 (Rfree = 0.000) for 1755 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 5: After refmac, R = 0.3040 (Rfree = 0.000) for 1724 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 4.26 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 1841 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 7 peptides. Score 0.261 Round 2: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.395 Round 3: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.395 Round 4: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.434 Round 5: 103 peptides, 15 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3793 restraints for refining 1707 atoms. 3421 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3051 (Rfree = 0.000) for 1707 atoms. Found 8 (8 requested) and removed 37 (4 requested) atoms. Cycle 7: After refmac, R = 0.2956 (Rfree = 0.000) for 1652 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 8: After refmac, R = 0.2560 (Rfree = 0.000) for 1629 atoms. Found 7 (7 requested) and removed 27 (3 requested) atoms. Cycle 9: After refmac, R = 0.3008 (Rfree = 0.000) for 1599 atoms. Found 7 (7 requested) and removed 25 (3 requested) atoms. Cycle 10: After refmac, R = 0.3093 (Rfree = 0.000) for 1569 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 1618 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 1646 seeds are put forward Round 1: 53 peptides, 13 chains. Longest chain 5 peptides. Score 0.176 Round 2: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.282 Round 3: 76 peptides, 16 chains. Longest chain 6 peptides. Score 0.263 Round 4: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.336 Round 5: 92 peptides, 16 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 5 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3809 restraints for refining 1685 atoms. 3521 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3549 (Rfree = 0.000) for 1685 atoms. Found 8 (8 requested) and removed 23 (4 requested) atoms. Cycle 12: After refmac, R = 0.3443 (Rfree = 0.000) for 1654 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 13: After refmac, R = 0.3503 (Rfree = 0.000) for 1634 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. Cycle 14: After refmac, R = 0.3605 (Rfree = 0.000) for 1605 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.3565 (Rfree = 0.000) for 1599 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 1688 seeds are put forward NCS extension: 0 residues added, 1688 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 6 peptides. Score 0.215 Round 2: 89 peptides, 18 chains. Longest chain 7 peptides. Score 0.297 Round 3: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.297 Round 4: 86 peptides, 18 chains. Longest chain 7 peptides. Score 0.275 Round 5: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.324 Taking the results from Round 5 Chains 15, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3550 restraints for refining 1590 atoms. 3305 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3819 (Rfree = 0.000) for 1590 atoms. Found 7 (7 requested) and removed 22 (3 requested) atoms. Cycle 17: After refmac, R = 0.3776 (Rfree = 0.000) for 1567 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 18: After refmac, R = 0.3679 (Rfree = 0.000) for 1552 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 19: After refmac, R = 0.3655 (Rfree = 0.000) for 1538 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 20: After refmac, R = 0.3597 (Rfree = 0.000) for 1533 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.82 Search for helices and strands: 0 residues in 0 chains, 1601 seeds are put forward NCS extension: 0 residues added, 1601 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 7 peptides. Score 0.209 Round 2: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.313 Round 3: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.333 Round 4: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.368 Round 5: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.324 Taking the results from Round 4 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3126 restraints for refining 1496 atoms. 2868 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3779 (Rfree = 0.000) for 1496 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 22: After refmac, R = 0.3770 (Rfree = 0.000) for 1471 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 23: After refmac, R = 0.3764 (Rfree = 0.000) for 1456 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 24: After refmac, R = 0.3710 (Rfree = 0.000) for 1446 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 25: After refmac, R = 0.3677 (Rfree = 0.000) for 1432 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.81 3.26 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward NCS extension: 0 residues added, 1494 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.239 Round 2: 72 peptides, 13 chains. Longest chain 8 peptides. Score 0.328 Round 3: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.326 Round 4: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.361 Round 5: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 4 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2935 restraints for refining 1430 atoms. 2681 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3820 (Rfree = 0.000) for 1430 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 27: After refmac, R = 0.3698 (Rfree = 0.000) for 1397 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 28: After refmac, R = 0.3624 (Rfree = 0.000) for 1375 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.3739 (Rfree = 0.000) for 1372 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 30: After refmac, R = 0.3603 (Rfree = 0.000) for 1361 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 1421 seeds are put forward NCS extension: 0 residues added, 1421 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 5 peptides. Score 0.200 Round 2: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.347 Round 3: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.319 Round 4: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.350 Round 5: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 5 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2939 restraints for refining 1484 atoms. 2664 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3757 (Rfree = 0.000) for 1484 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 32: After refmac, R = 0.3635 (Rfree = 0.000) for 1450 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 33: After refmac, R = 0.3583 (Rfree = 0.000) for 1424 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 34: After refmac, R = 0.3708 (Rfree = 0.000) for 1411 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 35: After refmac, R = 0.3439 (Rfree = 0.000) for 1399 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 1445 seeds are put forward NCS extension: 0 residues added, 1445 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 5 peptides. Score 0.209 Round 2: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.347 Round 3: 91 peptides, 14 chains. Longest chain 15 peptides. Score 0.428 Round 4: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.393 Round 5: 82 peptides, 12 chains. Longest chain 14 peptides. Score 0.428 Taking the results from Round 5 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2936 restraints for refining 1466 atoms. 2619 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3730 (Rfree = 0.000) for 1466 atoms. Found 6 (6 requested) and removed 38 (3 requested) atoms. Cycle 37: After refmac, R = 0.3814 (Rfree = 0.000) for 1427 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 38: After refmac, R = 0.3536 (Rfree = 0.000) for 1410 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 39: After refmac, R = 0.3556 (Rfree = 0.000) for 1400 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.3543 (Rfree = 0.000) for 1399 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1450 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.263 Round 2: 76 peptides, 15 chains. Longest chain 11 peptides. Score 0.294 Round 3: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.371 Round 4: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.347 Round 5: 84 peptides, 15 chains. Longest chain 12 peptides. Score 0.352 Taking the results from Round 3 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2906 restraints for refining 1406 atoms. 2644 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3736 (Rfree = 0.000) for 1406 atoms. Found 6 (6 requested) and removed 26 (3 requested) atoms. Cycle 42: After refmac, R = 0.3656 (Rfree = 0.000) for 1384 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 43: After refmac, R = 0.3805 (Rfree = 0.000) for 1372 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 44: After refmac, R = 0.3646 (Rfree = 0.000) for 1366 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.3790 (Rfree = 0.000) for 1364 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.74 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward NCS extension: 0 residues added, 1419 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.217 Round 2: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.272 Round 3: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.311 Round 4: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.304 Round 5: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 56, 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 2ouw-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2488 reflections ( 99.72 % complete ) and 2843 restraints for refining 1360 atoms. 2631 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3917 (Rfree = 0.000) for 1360 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3934 (Rfree = 0.000) for 1352 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3651 (Rfree = 0.000) for 1343 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3585 (Rfree = 0.000) for 1336 atoms. TimeTaking 31.05