Mon 24 Dec 08:00:11 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 2ozj-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-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/2ozj-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-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 08:00:16 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/2ozj-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6579 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.65 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: 75.275 4.000 Wilson plot Bfac: 81.82 1972 reflections ( 99.00 % complete ) and 0 restraints for refining 2030 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3423 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2845 (Rfree = 0.000) for 2030 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 2042 seeds are put forward NCS extension: 0 residues added, 2042 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.212 Round 2: 101 peptides, 18 chains. Longest chain 14 peptides. Score 0.403 Round 3: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.448 Round 4: 118 peptides, 20 chains. Longest chain 15 peptides. Score 0.462 Round 5: 117 peptides, 18 chains. Longest chain 14 peptides. Score 0.512 Taking the results from Round 5 Chains 18, Residues 99, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3821 restraints for refining 1647 atoms. 3413 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2414 (Rfree = 0.000) for 1647 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2329 (Rfree = 0.000) for 1592 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2247 (Rfree = 0.000) for 1564 atoms. Found 0 (7 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.2437 (Rfree = 0.000) for 1537 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2000 (Rfree = 0.000) for 1523 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 4.15 Search for helices and strands: 0 residues in 0 chains, 1574 seeds are put forward NCS extension: 0 residues added, 1574 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 12 peptides. Score 0.317 Round 2: 107 peptides, 21 chains. Longest chain 15 peptides. Score 0.353 Round 3: 104 peptides, 17 chains. Longest chain 18 peptides. Score 0.455 Round 4: 98 peptides, 16 chains. Longest chain 15 peptides. Score 0.443 Round 5: 100 peptides, 14 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 5 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3485 restraints for refining 1507 atoms. 3129 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2064 (Rfree = 0.000) for 1507 atoms. Found 6 (7 requested) and removed 13 (3 requested) atoms. Cycle 7: After refmac, R = 0.1843 (Rfree = 0.000) for 1494 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2017 (Rfree = 0.000) for 1481 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.1808 (Rfree = 0.000) for 1479 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.1804 (Rfree = 0.000) for 1470 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 4.12 Search for helices and strands: 0 residues in 0 chains, 1517 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1535 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 10 peptides. Score 0.264 Round 2: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.364 Round 3: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.375 Round 4: 95 peptides, 14 chains. Longest chain 12 peptides. Score 0.483 Round 5: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 4 Chains 14, Residues 81, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3402 restraints for refining 1467 atoms. 3069 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2127 (Rfree = 0.000) for 1467 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.2552 (Rfree = 0.000) for 1448 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.2307 (Rfree = 0.000) for 1434 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2643 (Rfree = 0.000) for 1426 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 15: After refmac, R = 0.2024 (Rfree = 0.000) for 1415 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 4.04 Search for helices and strands: 0 residues in 0 chains, 1475 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1488 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.326 Round 2: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.379 Round 3: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.382 Round 4: 100 peptides, 15 chains. Longest chain 19 peptides. Score 0.487 Round 5: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.499 Taking the results from Round 5 Chains 13, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3128 restraints for refining 1404 atoms. 2821 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3490 (Rfree = 0.000) for 1404 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 17: After refmac, R = 0.2073 (Rfree = 0.000) for 1382 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.1975 (Rfree = 0.000) for 1376 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2435 (Rfree = 0.000) for 1369 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2061 (Rfree = 0.000) for 1366 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 4.05 Search for helices and strands: 0 residues in 0 chains, 1411 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1429 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 7 peptides. Score 0.224 Round 2: 83 peptides, 14 chains. Longest chain 14 peptides. Score 0.397 Round 3: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.298 Round 4: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.377 Round 5: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.371 Taking the results from Round 2 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 2864 restraints for refining 1317 atoms. 2602 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2490 (Rfree = 0.000) for 1317 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 22: After refmac, R = 0.2526 (Rfree = 0.000) for 1306 atoms. Found 5 (6 requested) and removed 11 (3 requested) atoms. Cycle 23: After refmac, R = 0.1992 (Rfree = 0.000) for 1291 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2155 (Rfree = 0.000) for 1286 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 1287 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 1356 seeds are put forward NCS extension: 0 residues added, 1356 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.257 Round 2: 70 peptides, 12 chains. Longest chain 15 peptides. Score 0.363 Round 3: 79 peptides, 13 chains. Longest chain 13 peptides. Score 0.399 Round 4: 85 peptides, 15 chains. Longest chain 13 peptides. Score 0.379 Round 5: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.346 Taking the results from Round 3 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 2772 restraints for refining 1266 atoms. 2521 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2503 (Rfree = 0.000) for 1266 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 1252 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.1781 (Rfree = 0.000) for 1244 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.1705 (Rfree = 0.000) for 1239 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1721 (Rfree = 0.000) for 1237 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 4.16 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward NCS extension: 0 residues added, 1272 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.223 Round 2: 93 peptides, 16 chains. Longest chain 14 peptides. Score 0.407 Round 3: 86 peptides, 16 chains. Longest chain 14 peptides. Score 0.354 Round 4: 81 peptides, 13 chains. Longest chain 22 peptides. Score 0.414 Round 5: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 4 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 2938 restraints for refining 1361 atoms. 2645 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2259 (Rfree = 0.000) for 1361 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.1983 (Rfree = 0.000) for 1349 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.1871 (Rfree = 0.000) for 1340 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1697 (Rfree = 0.000) for 1336 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1647 (Rfree = 0.000) for 1333 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 4.09 Search for helices and strands: 0 residues in 0 chains, 1369 seeds are put forward NCS extension: 0 residues added, 1369 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.212 Round 2: 81 peptides, 15 chains. Longest chain 10 peptides. Score 0.348 Round 3: 70 peptides, 13 chains. Longest chain 12 peptides. Score 0.328 Round 4: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.336 Round 5: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 2 Chains 15, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3173 restraints for refining 1375 atoms. 2924 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1780 (Rfree = 0.000) for 1375 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 1371 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.1708 (Rfree = 0.000) for 1370 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1515 (Rfree = 0.000) for 1365 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1665 (Rfree = 0.000) for 1362 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 4.14 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 0 residues added, 1399 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.300 Round 2: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.323 Round 3: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.355 Round 4: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.387 Round 5: 83 peptides, 14 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3475 restraints for refining 1498 atoms. 3213 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1886 (Rfree = 0.000) for 1498 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.1924 (Rfree = 0.000) for 1478 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.1652 (Rfree = 0.000) for 1468 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1573 (Rfree = 0.000) for 1464 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1539 (Rfree = 0.000) for 1459 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 4.10 Search for helices and strands: 0 residues in 0 chains, 1498 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1523 seeds are put forward Round 1: 44 peptides, 11 chains. Longest chain 4 peptides. Score 0.167 Round 2: 51 peptides, 10 chains. Longest chain 15 peptides. Score 0.276 Round 3: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.262 Round 4: 61 peptides, 11 chains. Longest chain 15 peptides. Score 0.325 Round 5: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 55, 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 2ozj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1972 reflections ( 99.00 % complete ) and 3450 restraints for refining 1451 atoms. 3241 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1835 (Rfree = 0.000) for 1451 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1632 (Rfree = 0.000) for 1448 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1592 (Rfree = 0.000) for 1445 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1552 (Rfree = 0.000) for 1438 atoms. TimeTaking 25.33