null Mon 24 Dec 07:27:00 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ozj-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.4-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 07:27:04 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.4-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6503 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-3.4-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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.60 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 3.400 Wilson plot Bfac: 77.77 3159 reflections ( 99.37 % complete ) and 0 restraints for refining 2010 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3312 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3553 (Rfree = 0.000) for 2010 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 2015 seeds are put forward NCS extension: 0 residues added, 2015 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.309 Round 2: 131 peptides, 18 chains. Longest chain 20 peptides. Score 0.595 Round 3: 127 peptides, 18 chains. Longest chain 18 peptides. Score 0.572 Round 4: 126 peptides, 15 chains. Longest chain 20 peptides. Score 0.640 Round 5: 125 peptides, 16 chains. Longest chain 15 peptides. Score 0.611 Taking the results from Round 4 Chains 15, Residues 111, Estimated correctness of the model 41.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3942 restraints for refining 1658 atoms. 3513 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3232 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 2: After refmac, R = 0.3208 (Rfree = 0.000) for 1623 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 3: After refmac, R = 0.3168 (Rfree = 0.000) for 1607 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.3027 (Rfree = 0.000) for 1600 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.2958 (Rfree = 0.000) for 1583 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.70 Search for helices and strands: 0 residues in 0 chains, 1628 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 1655 seeds are put forward Round 1: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.464 Round 2: 128 peptides, 18 chains. Longest chain 22 peptides. Score 0.578 Round 3: 120 peptides, 15 chains. Longest chain 21 peptides. Score 0.608 Round 4: 116 peptides, 15 chains. Longest chain 19 peptides. Score 0.586 Round 5: 117 peptides, 17 chains. Longest chain 19 peptides. Score 0.539 Taking the results from Round 3 Chains 15, Residues 105, Estimated correctness of the model 31.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3463 restraints for refining 1520 atoms. 3058 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3299 (Rfree = 0.000) for 1520 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 7: After refmac, R = 0.2498 (Rfree = 0.000) for 1500 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2299 (Rfree = 0.000) for 1492 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2033 (Rfree = 0.000) for 1489 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2632 (Rfree = 0.000) for 1479 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.70 Search for helices and strands: 0 residues in 0 chains, 1528 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1547 seeds are put forward Round 1: 105 peptides, 18 chains. Longest chain 15 peptides. Score 0.431 Round 2: 122 peptides, 17 chains. Longest chain 16 peptides. Score 0.569 Round 3: 109 peptides, 14 chains. Longest chain 16 peptides. Score 0.571 Round 4: 115 peptides, 14 chains. Longest chain 18 peptides. Score 0.605 Round 5: 116 peptides, 16 chains. Longest chain 16 peptides. Score 0.560 Taking the results from Round 4 Chains 14, Residues 101, Estimated correctness of the model 30.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3362 restraints for refining 1498 atoms. 2972 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2818 (Rfree = 0.000) for 1498 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2181 (Rfree = 0.000) for 1487 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1986 (Rfree = 0.000) for 1479 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.1962 (Rfree = 0.000) for 1475 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.1950 (Rfree = 0.000) for 1468 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.72 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 1541 seeds are put forward Round 1: 112 peptides, 19 chains. Longest chain 9 peptides. Score 0.450 Round 2: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.584 Round 3: 131 peptides, 17 chains. Longest chain 21 peptides. Score 0.619 Round 4: 125 peptides, 18 chains. Longest chain 19 peptides. Score 0.561 Round 5: 133 peptides, 17 chains. Longest chain 17 peptides. Score 0.629 Taking the results from Round 5 Chains 17, Residues 116, Estimated correctness of the model 37.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3420 restraints for refining 1558 atoms. 2973 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2419 (Rfree = 0.000) for 1558 atoms. Found 8 (11 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2162 (Rfree = 0.000) for 1547 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2043 (Rfree = 0.000) for 1542 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.1995 (Rfree = 0.000) for 1537 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1972 (Rfree = 0.000) for 1531 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 1545 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1564 seeds are put forward Round 1: 104 peptides, 17 chains. Longest chain 13 peptides. Score 0.455 Round 2: 112 peptides, 16 chains. Longest chain 13 peptides. Score 0.536 Round 3: 115 peptides, 17 chains. Longest chain 12 peptides. Score 0.527 Round 4: 118 peptides, 17 chains. Longest chain 12 peptides. Score 0.545 Round 5: 114 peptides, 17 chains. Longest chain 13 peptides. Score 0.521 Taking the results from Round 4 Chains 17, Residues 101, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3633 restraints for refining 1599 atoms. 3246 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2356 (Rfree = 0.000) for 1599 atoms. Found 5 (12 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.2185 (Rfree = 0.000) for 1582 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2072 (Rfree = 0.000) for 1575 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 1568 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1986 (Rfree = 0.000) for 1562 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1586 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1601 seeds are put forward Round 1: 109 peptides, 18 chains. Longest chain 16 peptides. Score 0.459 Round 2: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.501 Round 3: 98 peptides, 15 chains. Longest chain 14 peptides. Score 0.473 Round 4: 96 peptides, 14 chains. Longest chain 14 peptides. Score 0.489 Round 5: 102 peptides, 16 chains. Longest chain 21 peptides. Score 0.471 Taking the results from Round 2 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3635 restraints for refining 1599 atoms. 3276 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2137 (Rfree = 0.000) for 1599 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.2027 (Rfree = 0.000) for 1591 atoms. Found 2 (12 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.1924 (Rfree = 0.000) for 1580 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2058 (Rfree = 0.000) for 1573 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.1945 (Rfree = 0.000) for 1568 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 1590 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1603 seeds are put forward Round 1: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.455 Round 2: 108 peptides, 16 chains. Longest chain 14 peptides. Score 0.510 Round 3: 111 peptides, 16 chains. Longest chain 20 peptides. Score 0.529 Round 4: 121 peptides, 18 chains. Longest chain 14 peptides. Score 0.537 Round 5: 104 peptides, 15 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 4 Chains 18, Residues 103, Estimated correctness of the model 6.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3529 restraints for refining 1607 atoms. 3135 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2332 (Rfree = 0.000) for 1607 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.2300 (Rfree = 0.000) for 1598 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2078 (Rfree = 0.000) for 1597 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2082 (Rfree = 0.000) for 1593 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2264 (Rfree = 0.000) for 1590 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1622 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1639 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.436 Round 2: 106 peptides, 14 chains. Longest chain 21 peptides. Score 0.553 Round 3: 106 peptides, 15 chains. Longest chain 22 peptides. Score 0.526 Round 4: 106 peptides, 16 chains. Longest chain 16 peptides. Score 0.497 Round 5: 113 peptides, 15 chains. Longest chain 23 peptides. Score 0.568 Taking the results from Round 5 Chains 16, Residues 98, Estimated correctness of the model 17.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3614 restraints for refining 1658 atoms. 3188 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2570 (Rfree = 0.000) for 1658 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.2665 (Rfree = 0.000) for 1648 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 38: After refmac, R = 0.2137 (Rfree = 0.000) for 1632 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2083 (Rfree = 0.000) for 1619 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2145 (Rfree = 0.000) for 1618 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 1646 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1667 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.280 Round 2: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.334 Round 3: 65 peptides, 11 chains. Longest chain 8 peptides. Score 0.358 Round 4: 74 peptides, 10 chains. Longest chain 16 peptides. Score 0.462 Round 5: 70 peptides, 10 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 4 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3828 restraints for refining 1602 atoms. 3582 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 1602 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 42: After refmac, R = 0.2292 (Rfree = 0.000) for 1596 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2615 (Rfree = 0.000) for 1593 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2469 (Rfree = 0.000) for 1592 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2006 (Rfree = 0.000) for 1593 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 1605 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 1609 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.248 Round 2: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.248 Round 3: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.304 Round 4: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.367 Round 5: 90 peptides, 13 chains. Longest chain 13 peptides. Score 0.479 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 77, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3159 reflections ( 99.37 % complete ) and 3467 restraints for refining 1562 atoms. 3172 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2400 (Rfree = 0.000) for 1562 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2593 (Rfree = 0.000) for 1542 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2273 (Rfree = 0.000) for 1526 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2026 (Rfree = 0.000) for 1517 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:52:07 GMT 2018 Job finished. TimeTaking 25.12 Used memory is bytes: 18298640