Mon 24 Dec 00:06:21 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 2ouw-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.8-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/2ouw-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.8-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 00:06:25 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/2ouw-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.8-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 153 and 0 Target number of residues in the AU: 153 Target solvent content: 0.6631 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-3.8-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2208 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: 108.355 3.800 Wilson plot Bfac: 87.14 2882 reflections ( 99.76 % complete ) and 0 restraints for refining 2439 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3796 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3554 (Rfree = 0.000) for 2439 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 4.35 Search for helices and strands: 0 residues in 0 chains, 2512 seeds are put forward NCS extension: 0 residues added, 2512 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.256 Round 2: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.355 Round 3: 110 peptides, 18 chains. Longest chain 14 peptides. Score 0.438 Round 4: 125 peptides, 18 chains. Longest chain 11 peptides. Score 0.526 Round 5: 129 peptides, 19 chains. Longest chain 12 peptides. Score 0.523 Taking the results from Round 4 Chains 18, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 4647 restraints for refining 1985 atoms. 4237 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3044 (Rfree = 0.000) for 1985 atoms. Found 10 (10 requested) and removed 55 (5 requested) atoms. Cycle 2: After refmac, R = 0.3268 (Rfree = 0.000) for 1889 atoms. Found 10 (10 requested) and removed 63 (5 requested) atoms. Cycle 3: After refmac, R = 0.3178 (Rfree = 0.000) for 1804 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 4: After refmac, R = 0.2663 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 5: After refmac, R = 0.3146 (Rfree = 0.000) for 1764 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 1855 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1867 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 8 peptides. Score 0.266 Round 2: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.365 Round 3: 105 peptides, 18 chains. Longest chain 15 peptides. Score 0.406 Round 4: 102 peptides, 16 chains. Longest chain 12 peptides. Score 0.442 Round 5: 97 peptides, 14 chains. Longest chain 13 peptides. Score 0.466 Taking the results from Round 5 Chains 14, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 4191 restraints for refining 1766 atoms. 3873 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2906 (Rfree = 0.000) for 1766 atoms. Found 9 (9 requested) and removed 29 (4 requested) atoms. Cycle 7: After refmac, R = 0.2995 (Rfree = 0.000) for 1732 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.2888 (Rfree = 0.000) for 1718 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 9: After refmac, R = 0.3061 (Rfree = 0.000) for 1702 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2939 (Rfree = 0.000) for 1695 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 1790 seeds are put forward NCS extension: 0 residues added, 1790 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.241 Round 2: 98 peptides, 21 chains. Longest chain 9 peptides. Score 0.272 Round 3: 97 peptides, 19 chains. Longest chain 7 peptides. Score 0.324 Round 4: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.434 Round 5: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3795 restraints for refining 1681 atoms. 3473 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3021 (Rfree = 0.000) for 1681 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 12: After refmac, R = 0.3043 (Rfree = 0.000) for 1664 atoms. Found 9 (9 requested) and removed 40 (4 requested) atoms. Cycle 13: After refmac, R = 0.3034 (Rfree = 0.000) for 1625 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 14: After refmac, R = 0.3191 (Rfree = 0.000) for 1601 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 15: After refmac, R = 0.3253 (Rfree = 0.000) for 1583 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 1670 seeds are put forward NCS extension: 0 residues added, 1670 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 7 peptides. Score 0.219 Round 2: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.327 Round 3: 84 peptides, 16 chains. Longest chain 13 peptides. Score 0.322 Round 4: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.320 Round 5: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.255 Taking the results from Round 2 Chains 17, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3187 restraints for refining 1519 atoms. 2916 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3262 (Rfree = 0.000) for 1519 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 17: After refmac, R = 0.3301 (Rfree = 0.000) for 1499 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.3394 (Rfree = 0.000) for 1496 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.3456 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.3161 (Rfree = 0.000) for 1478 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.82 Search for helices and strands: 0 residues in 0 chains, 1555 seeds are put forward NCS extension: 0 residues added, 1555 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 7 peptides. Score 0.208 Round 2: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.304 Round 3: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.326 Round 4: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.266 Round 5: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 5 Chains 14, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3338 restraints for refining 1535 atoms. 3104 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3356 (Rfree = 0.000) for 1535 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 22: After refmac, R = 0.3280 (Rfree = 0.000) for 1511 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.3654 (Rfree = 0.000) for 1497 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 24: After refmac, R = 0.3337 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.3604 (Rfree = 0.000) for 1483 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 3.44 Search for helices and strands: 0 residues in 0 chains, 1525 seeds are put forward NCS extension: 0 residues added, 1525 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.220 Round 2: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.249 Round 3: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.309 Round 4: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.309 Round 5: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.262 Taking the results from Round 4 Chains 12, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3270 restraints for refining 1503 atoms. 3070 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3578 (Rfree = 0.000) for 1503 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 27: After refmac, R = 0.3637 (Rfree = 0.000) for 1477 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 28: After refmac, R = 0.3539 (Rfree = 0.000) for 1465 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.3494 (Rfree = 0.000) for 1463 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.3584 (Rfree = 0.000) for 1460 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.94 3.41 Search for helices and strands: 0 residues in 0 chains, 1499 seeds are put forward NCS extension: 0 residues added, 1499 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.272 Round 2: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.304 Round 3: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.318 Round 4: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.331 Round 5: 96 peptides, 18 chains. Longest chain 7 peptides. Score 0.346 Taking the results from Round 5 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3020 restraints for refining 1513 atoms. 2705 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3550 (Rfree = 0.000) for 1513 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 32: After refmac, R = 0.3518 (Rfree = 0.000) for 1490 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.3361 (Rfree = 0.000) for 1480 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.3231 (Rfree = 0.000) for 1470 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.3178 (Rfree = 0.000) for 1471 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 1505 seeds are put forward NCS extension: 0 residues added, 1505 seeds are put forward Round 1: 74 peptides, 18 chains. Longest chain 5 peptides. Score 0.183 Round 2: 91 peptides, 18 chains. Longest chain 10 peptides. Score 0.311 Round 3: 84 peptides, 16 chains. Longest chain 7 peptides. Score 0.322 Round 4: 97 peptides, 18 chains. Longest chain 12 peptides. Score 0.353 Round 5: 93 peptides, 17 chains. Longest chain 8 peptides. Score 0.355 Taking the results from Round 5 Chains 17, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3275 restraints for refining 1566 atoms. 2988 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3549 (Rfree = 0.000) for 1566 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 37: After refmac, R = 0.3505 (Rfree = 0.000) for 1547 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.3315 (Rfree = 0.000) for 1537 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.3563 (Rfree = 0.000) for 1531 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 40: After refmac, R = 0.3376 (Rfree = 0.000) for 1524 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 1576 seeds are put forward NCS extension: 0 residues added, 1576 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.219 Round 2: 67 peptides, 13 chains. Longest chain 6 peptides. Score 0.291 Round 3: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.313 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.338 Round 5: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2882 reflections ( 99.76 % complete ) and 3453 restraints for refining 1604 atoms. 3217 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3762 (Rfree = 0.000) for 1604 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 42: After refmac, R = 0.3610 (Rfree = 0.000) for 1578 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 43: After refmac, R = 0.3452 (Rfree = 0.000) for 1563 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 44: After refmac, R = 0.3725 (Rfree = 0.000) for 1553 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.3481 (Rfree = 0.000) for 1548 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.86 Search for helices and strands: 0 residues in 0 chains, 1583 seeds are put forward NCS extension: 0 residues added, 1583 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.186 Round 2: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.244 Round 3: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.270 Round 4: 63 peptides, 13 chains. Longest chain 9 peptides. Score 0.260 Round 5: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.313 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, 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 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2882 reflections ( 99.76 % complete ) and 3075 restraints for refining 1536 atoms. 2860 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3718 (Rfree = 0.000) for 1536 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3492 (Rfree = 0.000) for 1531 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3494 (Rfree = 0.000) for 1523 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3420 (Rfree = 0.000) for 1517 atoms. TimeTaking 26.7