Sun 23 Dec 22:23:04 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ozj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:13 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/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-4.0-parrot-hancs/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-hancs.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-hancs.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 2009 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3401 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 2009 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward NCS extension: 0 residues added, 2016 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 6 peptides. Score 0.255 Round 2: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.419 Round 3: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.361 Round 4: 121 peptides, 19 chains. Longest chain 11 peptides. Score 0.510 Round 5: 122 peptides, 21 chains. Longest chain 11 peptides. Score 0.460 Taking the results from Round 4 Chains 19, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3804 restraints for refining 1647 atoms. 3415 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2320 (Rfree = 0.000) for 1647 atoms. Found 4 (7 requested) and removed 10 (3 requested) atoms. Cycle 2: After refmac, R = 0.2154 (Rfree = 0.000) for 1618 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2130 (Rfree = 0.000) for 1599 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2050 (Rfree = 0.000) for 1592 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2056 (Rfree = 0.000) for 1587 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 1620 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 1632 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 10 peptides. Score 0.280 Round 2: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.392 Round 3: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.450 Round 4: 104 peptides, 17 chains. Longest chain 10 peptides. Score 0.455 Round 5: 108 peptides, 17 chains. Longest chain 10 peptides. Score 0.482 Taking the results from Round 5 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3803 restraints for refining 1586 atoms. 3456 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 1586 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 7: After refmac, R = 0.1997 (Rfree = 0.000) for 1567 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.2211 (Rfree = 0.000) for 1545 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.2192 (Rfree = 0.000) for 1542 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.1693 (Rfree = 0.000) for 1537 atoms. Found 2 (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, 1571 seeds are put forward NCS extension: 0 residues added, 1571 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 6 peptides. Score 0.234 Round 2: 105 peptides, 20 chains. Longest chain 11 peptides. Score 0.370 Round 3: 109 peptides, 21 chains. Longest chain 8 peptides. Score 0.368 Round 4: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.415 Round 5: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.448 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3866 restraints for refining 1604 atoms. 3539 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2120 (Rfree = 0.000) for 1604 atoms. Found 3 (7 requested) and removed 13 (3 requested) atoms. Cycle 12: After refmac, R = 0.1988 (Rfree = 0.000) for 1588 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.1838 (Rfree = 0.000) for 1584 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.1956 (Rfree = 0.000) for 1581 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1867 (Rfree = 0.000) for 1577 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 4.14 Search for helices and strands: 0 residues in 0 chains, 1593 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1609 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 6 peptides. Score 0.237 Round 2: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.354 Round 3: 94 peptides, 16 chains. Longest chain 12 peptides. Score 0.414 Round 4: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.405 Round 5: 103 peptides, 16 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 5 Chains 16, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3873 restraints for refining 1617 atoms. 3541 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2138 (Rfree = 0.000) for 1617 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2071 (Rfree = 0.000) for 1606 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.1897 (Rfree = 0.000) for 1599 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.1852 (Rfree = 0.000) for 1592 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1749 (Rfree = 0.000) for 1587 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 4.18 Search for helices and strands: 0 residues in 0 chains, 1610 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1622 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 5 peptides. Score 0.219 Round 2: 77 peptides, 15 chains. Longest chain 7 peptides. Score 0.316 Round 3: 90 peptides, 15 chains. Longest chain 17 peptides. Score 0.416 Round 4: 102 peptides, 16 chains. Longest chain 17 peptides. Score 0.471 Round 5: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 4 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 4059 restraints for refining 1647 atoms. 3731 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1984 (Rfree = 0.000) for 1647 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.1882 (Rfree = 0.000) for 1640 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.1846 (Rfree = 0.000) for 1635 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.1660 (Rfree = 0.000) for 1629 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1659 (Rfree = 0.000) for 1623 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 4.17 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: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.280 Round 2: 79 peptides, 14 chains. Longest chain 14 peptides. Score 0.366 Round 3: 82 peptides, 14 chains. Longest chain 16 peptides. Score 0.389 Round 4: 95 peptides, 17 chains. Longest chain 17 peptides. Score 0.390 Round 5: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.421 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 4077 restraints for refining 1646 atoms. 3777 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1961 (Rfree = 0.000) for 1646 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.1976 (Rfree = 0.000) for 1630 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2243 (Rfree = 0.000) for 1613 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1870 (Rfree = 0.000) for 1597 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.1682 (Rfree = 0.000) for 1587 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 4.13 Search for helices and strands: 0 residues in 0 chains, 1625 seeds are put forward NCS extension: 0 residues added, 1625 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 7 peptides. Score 0.223 Round 2: 82 peptides, 16 chains. Longest chain 14 peptides. Score 0.322 Round 3: 84 peptides, 14 chains. Longest chain 12 peptides. Score 0.404 Round 4: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.353 Round 5: 66 peptides, 11 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 3 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3615 restraints for refining 1481 atoms. 3349 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1980 (Rfree = 0.000) for 1481 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2119 (Rfree = 0.000) for 1478 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2200 (Rfree = 0.000) for 1477 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2017 (Rfree = 0.000) for 1476 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.1821 (Rfree = 0.000) for 1473 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 1497 seeds are put forward NCS extension: 0 residues added, 1497 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.234 Round 2: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.315 Round 3: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.315 Round 4: 65 peptides, 10 chains. Longest chain 15 peptides. Score 0.394 Round 5: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.334 Taking the results from Round 4 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3574 restraints for refining 1467 atoms. 3364 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1796 (Rfree = 0.000) for 1467 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.1817 (Rfree = 0.000) for 1460 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.1859 (Rfree = 0.000) for 1458 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2236 (Rfree = 0.000) for 1457 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1643 (Rfree = 0.000) for 1459 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 4.13 Search for helices and strands: 0 residues in 0 chains, 1466 seeds are put forward NCS extension: 0 residues added, 1466 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.216 Round 2: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.286 Round 3: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.303 Round 4: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.264 Round 5: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.306 Taking the results from Round 5 Chains 12, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1972 reflections ( 99.00 % complete ) and 3555 restraints for refining 1452 atoms. 3363 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1887 (Rfree = 0.000) for 1452 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 42: After refmac, R = 0.1872 (Rfree = 0.000) for 1450 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.1784 (Rfree = 0.000) for 1447 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.1728 (Rfree = 0.000) for 1445 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1704 (Rfree = 0.000) for 1442 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 4.14 Search for helices and strands: 0 residues in 0 chains, 1461 seeds are put forward NCS extension: 0 residues added, 1461 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 8 peptides. Score 0.225 Round 2: 72 peptides, 15 chains. Longest chain 10 peptides. Score 0.274 Round 3: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.332 Round 4: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.336 Round 5: 60 peptides, 12 chains. Longest chain 10 peptides. Score 0.280 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 58, 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 3386 restraints for refining 1431 atoms. 3167 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1965 (Rfree = 0.000) for 1431 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1711 (Rfree = 0.000) for 1426 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1768 (Rfree = 0.000) for 1419 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1958 (Rfree = 0.000) for 1413 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. TimeTaking 29.38