Mon 24 Dec 00:40:55 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-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 00:41:00 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-4.0-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 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-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-4.0-parrot-mrncs.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 2444 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3919 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3582 (Rfree = 0.000) for 2444 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.95 4.58 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: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.242 Round 2: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.375 Round 3: 102 peptides, 17 chains. Longest chain 9 peptides. Score 0.415 Round 4: 109 peptides, 14 chains. Longest chain 17 peptides. Score 0.536 Round 5: 111 peptides, 14 chains. Longest chain 17 peptides. Score 0.547 Taking the results from Round 5 Chains 14, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 4560 restraints for refining 1906 atoms. 4186 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3294 (Rfree = 0.000) for 1906 atoms. Found 7 (9 requested) and removed 30 (4 requested) atoms. Cycle 2: After refmac, R = 0.3147 (Rfree = 0.000) for 1839 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 3: After refmac, R = 0.3096 (Rfree = 0.000) for 1790 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 4: After refmac, R = 0.3020 (Rfree = 0.000) for 1756 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 5: After refmac, R = 0.3387 (Rfree = 0.000) for 1717 atoms. Found 8 (8 requested) and removed 30 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 1795 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1817 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 7 peptides. Score 0.218 Round 2: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.346 Round 3: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.351 Round 4: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.395 Round 5: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.431 Taking the results from Round 5 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3805 restraints for refining 1682 atoms. 3459 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3417 (Rfree = 0.000) for 1682 atoms. Found 7 (7 requested) and removed 42 (3 requested) atoms. Cycle 7: After refmac, R = 0.3406 (Rfree = 0.000) for 1630 atoms. Found 7 (7 requested) and removed 32 (3 requested) atoms. Cycle 8: After refmac, R = 0.3420 (Rfree = 0.000) for 1595 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 9: After refmac, R = 0.3370 (Rfree = 0.000) for 1577 atoms. Found 7 (7 requested) and removed 49 (3 requested) atoms. Cycle 10: After refmac, R = 0.3389 (Rfree = 0.000) for 1529 atoms. Found 7 (7 requested) and removed 29 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 1582 seeds are put forward NCS extension: 0 residues added, 1582 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.249 Round 2: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.395 Round 3: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.366 Round 4: 92 peptides, 14 chains. Longest chain 10 peptides. Score 0.435 Round 5: 92 peptides, 14 chains. Longest chain 18 peptides. Score 0.435 Taking the results from Round 5 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3537 restraints for refining 1653 atoms. 3214 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3664 (Rfree = 0.000) for 1653 atoms. Found 7 (7 requested) and removed 24 (3 requested) atoms. Cycle 12: After refmac, R = 0.3625 (Rfree = 0.000) for 1624 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 13: After refmac, R = 0.3575 (Rfree = 0.000) for 1604 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 14: After refmac, R = 0.3795 (Rfree = 0.000) for 1589 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 15: After refmac, R = 0.3598 (Rfree = 0.000) for 1573 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1653 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 9 peptides. Score 0.244 Round 2: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.354 Round 3: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.350 Round 4: 85 peptides, 14 chains. Longest chain 14 peptides. Score 0.389 Round 5: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.359 Taking the results from Round 4 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3302 restraints for refining 1553 atoms. 3032 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3867 (Rfree = 0.000) for 1553 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 17: After refmac, R = 0.3202 (Rfree = 0.000) for 1524 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 18: After refmac, R = 0.3728 (Rfree = 0.000) for 1516 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 19: After refmac, R = 0.3508 (Rfree = 0.000) for 1505 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 20: After refmac, R = 0.3572 (Rfree = 0.000) for 1494 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 1554 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 1569 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 8 peptides. Score 0.253 Round 2: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.410 Round 3: 87 peptides, 14 chains. Longest chain 10 peptides. Score 0.402 Round 4: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.430 Round 5: 93 peptides, 14 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 3178 restraints for refining 1508 atoms. 2876 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3758 (Rfree = 0.000) for 1508 atoms. Found 7 (7 requested) and removed 27 (3 requested) atoms. Cycle 22: After refmac, R = 0.3804 (Rfree = 0.000) for 1474 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 23: After refmac, R = 0.3830 (Rfree = 0.000) for 1457 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.3773 (Rfree = 0.000) for 1438 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 25: After refmac, R = 0.3340 (Rfree = 0.000) for 1428 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.95 Search for helices and strands: 0 residues in 0 chains, 1483 seeds are put forward NCS extension: 0 residues added, 1483 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.229 Round 2: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.306 Round 3: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.341 Round 4: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.345 Round 5: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.285 Taking the results from Round 4 Chains 15, Residues 68, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2962 restraints for refining 1441 atoms. 2686 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3929 (Rfree = 0.000) for 1441 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 27: After refmac, R = 0.3957 (Rfree = 0.000) for 1409 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 28: After refmac, R = 0.3868 (Rfree = 0.000) for 1387 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 29: After refmac, R = 0.3902 (Rfree = 0.000) for 1374 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 30: After refmac, R = 0.3279 (Rfree = 0.000) for 1367 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 1432 seeds are put forward NCS extension: 0 residues added, 1432 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.186 Round 2: 79 peptides, 16 chains. Longest chain 7 peptides. Score 0.285 Round 3: 83 peptides, 15 chains. Longest chain 12 peptides. Score 0.345 Round 4: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.359 Round 5: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 4 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2833 restraints for refining 1387 atoms. 2568 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3886 (Rfree = 0.000) for 1387 atoms. Found 6 (6 requested) and removed 29 (3 requested) atoms. Cycle 32: After refmac, R = 0.3756 (Rfree = 0.000) for 1356 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 33: After refmac, R = 0.3669 (Rfree = 0.000) for 1342 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 34: After refmac, R = 0.3778 (Rfree = 0.000) for 1328 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 35: After refmac, R = 0.3696 (Rfree = 0.000) for 1322 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 1366 seeds are put forward NCS extension: 0 residues added, 1366 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.208 Round 2: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.298 Round 3: 86 peptides, 16 chains. Longest chain 7 peptides. Score 0.336 Round 4: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.287 Round 5: 73 peptides, 14 chains. Longest chain 7 peptides. Score 0.304 Taking the results from Round 3 Chains 16, Residues 70, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2743 restraints for refining 1368 atoms. 2457 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3706 (Rfree = 0.000) for 1368 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 37: After refmac, R = 0.3565 (Rfree = 0.000) for 1353 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 38: After refmac, R = 0.3625 (Rfree = 0.000) for 1335 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 39: After refmac, R = 0.3588 (Rfree = 0.000) for 1326 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.3702 (Rfree = 0.000) for 1321 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 1383 seeds are put forward NCS extension: 0 residues added, 1383 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.230 Round 2: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.283 Round 3: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.275 Round 4: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.296 Round 5: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.281 Taking the results from Round 4 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2488 reflections ( 99.72 % complete ) and 2525 restraints for refining 1263 atoms. 2344 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3890 (Rfree = 0.000) for 1263 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 42: After refmac, R = 0.3603 (Rfree = 0.000) for 1243 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 43: After refmac, R = 0.3579 (Rfree = 0.000) for 1230 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 44: After refmac, R = 0.3626 (Rfree = 0.000) for 1220 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 45: After refmac, R = 0.3494 (Rfree = 0.000) for 1216 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward NCS extension: 0 residues added, 1268 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 2: 52 peptides, 10 chains. Longest chain 11 peptides. Score 0.275 Round 3: 50 peptides, 10 chains. Longest chain 9 peptides. Score 0.258 Round 4: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.322 Round 5: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 49, 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 2362 restraints for refining 1228 atoms. 2175 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3881 (Rfree = 0.000) for 1228 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3735 (Rfree = 0.000) for 1221 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3666 (Rfree = 0.000) for 1213 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3878 (Rfree = 0.000) for 1205 atoms. TimeTaking 30.93