Sun 23 Dec 23:50:34 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 2ozj-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.4-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/2ozj-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.4-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 ============================================================ Sun 23 Dec 23:50:39 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/2ozj-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-3.4-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 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-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.4-parrot-mrncs.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 2025 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3235 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2839 (Rfree = 0.000) for 2025 atoms. Found 8 (15 requested) and removed 24 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 0 residues added, 2033 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.441 Round 2: 148 peptides, 20 chains. Longest chain 14 peptides. Score 0.638 Round 3: 148 peptides, 18 chains. Longest chain 20 peptides. Score 0.680 Round 4: 156 peptides, 19 chains. Longest chain 20 peptides. Score 0.695 Round 5: 163 peptides, 15 chains. Longest chain 33 peptides. Score 0.788 Taking the results from Round 5 Chains 15, Residues 148, Estimated correctness of the model 77.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3400 restraints for refining 1657 atoms. 2745 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2683 (Rfree = 0.000) for 1657 atoms. Found 8 (12 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.2571 (Rfree = 0.000) for 1626 atoms. Found 2 (12 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.2555 (Rfree = 0.000) for 1606 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 4: After refmac, R = 0.2524 (Rfree = 0.000) for 1592 atoms. Found 3 (11 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.2416 (Rfree = 0.000) for 1576 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 1591 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 1613 seeds are put forward Round 1: 134 peptides, 21 chains. Longest chain 18 peptides. Score 0.537 Round 2: 131 peptides, 14 chains. Longest chain 22 peptides. Score 0.685 Round 3: 140 peptides, 18 chains. Longest chain 23 peptides. Score 0.642 Round 4: 137 peptides, 16 chains. Longest chain 21 peptides. Score 0.671 Round 5: 132 peptides, 16 chains. Longest chain 16 peptides. Score 0.647 Taking the results from Round 2 Chains 14, Residues 117, Estimated correctness of the model 53.9 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3540 restraints for refining 1620 atoms. 3018 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2563 (Rfree = 0.000) for 1620 atoms. Found 9 (11 requested) and removed 21 (6 requested) atoms. Cycle 7: After refmac, R = 0.2946 (Rfree = 0.000) for 1596 atoms. Found 11 (11 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2558 (Rfree = 0.000) for 1576 atoms. Found 4 (11 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2828 (Rfree = 0.000) for 1560 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2406 (Rfree = 0.000) for 1557 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1578 seeds are put forward NCS extension: 35 residues added (7 deleted due to clashes), 1613 seeds are put forward Round 1: 125 peptides, 21 chains. Longest chain 20 peptides. Score 0.480 Round 2: 136 peptides, 19 chains. Longest chain 25 peptides. Score 0.598 Round 3: 131 peptides, 17 chains. Longest chain 18 peptides. Score 0.619 Round 4: 145 peptides, 18 chains. Longest chain 28 peptides. Score 0.666 Round 5: 146 peptides, 19 chains. Longest chain 24 peptides. Score 0.650 Taking the results from Round 4 Chains 18, Residues 127, Estimated correctness of the model 48.7 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3244 restraints for refining 1571 atoms. 2693 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2687 (Rfree = 0.000) for 1571 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 12: After refmac, R = 0.2501 (Rfree = 0.000) for 1560 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2235 (Rfree = 0.000) for 1558 atoms. Found 0 (10 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2304 (Rfree = 0.000) for 1546 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 1541 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 1566 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 1606 seeds are put forward Round 1: 114 peptides, 18 chains. Longest chain 21 peptides. Score 0.493 Round 2: 135 peptides, 16 chains. Longest chain 28 peptides. Score 0.661 Round 3: 147 peptides, 20 chains. Longest chain 20 peptides. Score 0.633 Round 4: 141 peptides, 15 chains. Longest chain 28 peptides. Score 0.709 Round 5: 133 peptides, 17 chains. Longest chain 30 peptides. Score 0.629 Taking the results from Round 4 Chains 15, Residues 126, Estimated correctness of the model 60.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3527 restraints for refining 1594 atoms. 3038 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2648 (Rfree = 0.000) for 1594 atoms. Found 9 (11 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.2607 (Rfree = 0.000) for 1584 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2628 (Rfree = 0.000) for 1583 atoms. Found 6 (9 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.3099 (Rfree = 0.000) for 1568 atoms. Found 9 (9 requested) and removed 16 (5 requested) atoms. Cycle 20: After refmac, R = 0.2845 (Rfree = 0.000) for 1552 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1601 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 1639 seeds are put forward Round 1: 103 peptides, 19 chains. Longest chain 14 peptides. Score 0.386 Round 2: 117 peptides, 17 chains. Longest chain 27 peptides. Score 0.539 Round 3: 116 peptides, 14 chains. Longest chain 23 peptides. Score 0.611 Round 4: 106 peptides, 17 chains. Longest chain 19 peptides. Score 0.468 Round 5: 115 peptides, 16 chains. Longest chain 19 peptides. Score 0.554 Taking the results from Round 3 Chains 14, Residues 102, Estimated correctness of the model 32.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3489 restraints for refining 1538 atoms. 3095 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2782 (Rfree = 0.000) for 1538 atoms. Found 4 (9 requested) and removed 19 (5 requested) atoms. Cycle 22: After refmac, R = 0.2650 (Rfree = 0.000) for 1518 atoms. Found 2 (9 requested) and removed 24 (5 requested) atoms. Cycle 23: After refmac, R = 0.2780 (Rfree = 0.000) for 1493 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2387 (Rfree = 0.000) for 1491 atoms. Found 4 (9 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2323 (Rfree = 0.000) for 1485 atoms. Found 0 (9 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 1522 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1541 seeds are put forward Round 1: 92 peptides, 17 chains. Longest chain 14 peptides. Score 0.367 Round 2: 98 peptides, 14 chains. Longest chain 21 peptides. Score 0.503 Round 3: 113 peptides, 16 chains. Longest chain 18 peptides. Score 0.542 Round 4: 109 peptides, 16 chains. Longest chain 24 peptides. Score 0.517 Round 5: 97 peptides, 14 chains. Longest chain 19 peptides. Score 0.496 Taking the results from Round 3 Chains 16, Residues 97, Estimated correctness of the model 8.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3493 restraints for refining 1530 atoms. 3121 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2549 (Rfree = 0.000) for 1530 atoms. Found 3 (9 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2684 (Rfree = 0.000) for 1507 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2242 (Rfree = 0.000) for 1503 atoms. Found 3 (9 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2178 (Rfree = 0.000) for 1499 atoms. Found 4 (9 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.2124 (Rfree = 0.000) for 1495 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 1534 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1550 seeds are put forward Round 1: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.350 Round 2: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.445 Round 3: 108 peptides, 16 chains. Longest chain 13 peptides. Score 0.510 Round 4: 104 peptides, 16 chains. Longest chain 12 peptides. Score 0.484 Round 5: 107 peptides, 16 chains. Longest chain 13 peptides. Score 0.504 Taking the results from Round 3 Chains 16, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3576 restraints for refining 1554 atoms. 3224 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2318 (Rfree = 0.000) for 1554 atoms. Found 1 (9 requested) and removed 12 (5 requested) atoms. Cycle 32: After refmac, R = 0.2734 (Rfree = 0.000) for 1541 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2266 (Rfree = 0.000) for 1535 atoms. Found 7 (9 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2476 (Rfree = 0.000) for 1528 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2869 (Rfree = 0.000) for 1526 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 1564 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1577 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 9 peptides. Score 0.269 Round 2: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.404 Round 3: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.407 Round 4: 106 peptides, 15 chains. Longest chain 13 peptides. Score 0.526 Round 5: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.466 Taking the results from Round 4 Chains 15, Residues 91, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3495 restraints for refining 1543 atoms. 3146 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2364 (Rfree = 0.000) for 1543 atoms. Found 7 (9 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.2191 (Rfree = 0.000) for 1539 atoms. Found 8 (9 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2191 (Rfree = 0.000) for 1537 atoms. Found 5 (9 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.2378 (Rfree = 0.000) for 1532 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.3083 (Rfree = 0.000) for 1528 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 1547 seeds are put forward NCS extension: 0 residues added, 1547 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.304 Round 2: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.405 Round 3: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.375 Round 4: 95 peptides, 13 chains. Longest chain 15 peptides. Score 0.512 Round 5: 93 peptides, 13 chains. Longest chain 15 peptides. Score 0.499 Taking the results from Round 4 Chains 13, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3159 reflections ( 99.37 % complete ) and 3552 restraints for refining 1553 atoms. 3237 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2422 (Rfree = 0.000) for 1553 atoms. Found 6 (9 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.2360 (Rfree = 0.000) for 1547 atoms. Found 8 (9 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2353 (Rfree = 0.000) for 1544 atoms. Found 6 (9 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2607 (Rfree = 0.000) for 1542 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2874 (Rfree = 0.000) for 1538 atoms. Found 9 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 1565 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 1587 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.280 Round 2: 78 peptides, 13 chains. Longest chain 15 peptides. Score 0.392 Round 3: 87 peptides, 14 chains. Longest chain 12 peptides. Score 0.426 Round 4: 91 peptides, 12 chains. Longest chain 16 peptides. Score 0.516 Round 5: 86 peptides, 12 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 79, 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 3379 restraints for refining 1504 atoms. 3075 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2879 (Rfree = 0.000) for 1504 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2748 (Rfree = 0.000) for 1491 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2676 (Rfree = 0.000) for 1481 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3015 (Rfree = 0.000) for 1472 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 24.43