Mon 24 Dec 00:38:45 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 2od4-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-4.0-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/2od4-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-4.0-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 00:38:50 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/2od4-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-4.0-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 101 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 202 Adjusted target solvent content: 0.48 Input MTZ file: 2od4-4.0-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1616 target number of atoms Had to go as low as 0.70 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: 28.889 4.000 Wilson plot Bfac: 80.16 1758 reflections ( 98.27 % complete ) and 0 restraints for refining 1782 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3300 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2168 (Rfree = 0.000) for 1782 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward NCS extension: 0 residues added, 1808 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.229 Round 2: 90 peptides, 13 chains. Longest chain 14 peptides. Score 0.482 Round 3: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.470 Round 4: 105 peptides, 14 chains. Longest chain 17 peptides. Score 0.551 Round 5: 108 peptides, 14 chains. Longest chain 21 peptides. Score 0.569 Taking the results from Round 5 Chains 14, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3370 restraints for refining 1458 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2306 (Rfree = 0.000) for 1458 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2140 (Rfree = 0.000) for 1442 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2068 (Rfree = 0.000) for 1432 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.1984 (Rfree = 0.000) for 1423 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.1937 (Rfree = 0.000) for 1416 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 1466 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1488 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 11 peptides. Score 0.348 Round 2: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.490 Round 3: 98 peptides, 14 chains. Longest chain 12 peptides. Score 0.506 Round 4: 99 peptides, 12 chains. Longest chain 15 peptides. Score 0.570 Round 5: 101 peptides, 13 chains. Longest chain 16 peptides. Score 0.554 Taking the results from Round 4 Chains 12, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3517 restraints for refining 1459 atoms. 3181 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2088 (Rfree = 0.000) for 1459 atoms. Found 1 (6 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.1953 (Rfree = 0.000) for 1441 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.1872 (Rfree = 0.000) for 1434 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.1832 (Rfree = 0.000) for 1424 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1805 (Rfree = 0.000) for 1418 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 1460 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1478 seeds are put forward Round 1: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.363 Round 2: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.465 Round 3: 102 peptides, 15 chains. Longest chain 16 peptides. Score 0.503 Round 4: 103 peptides, 15 chains. Longest chain 13 peptides. Score 0.510 Round 5: 94 peptides, 13 chains. Longest chain 16 peptides. Score 0.509 Taking the results from Round 4 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3459 restraints for refining 1459 atoms. 3122 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1954 (Rfree = 0.000) for 1459 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 12: After refmac, R = 0.1905 (Rfree = 0.000) for 1449 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1801 (Rfree = 0.000) for 1444 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.1792 (Rfree = 0.000) for 1438 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2125 (Rfree = 0.000) for 1434 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 1469 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1482 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 7 peptides. Score 0.263 Round 2: 93 peptides, 14 chains. Longest chain 10 peptides. Score 0.472 Round 3: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.417 Round 4: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.455 Round 5: 92 peptides, 16 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 2 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3512 restraints for refining 1459 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2507 (Rfree = 0.000) for 1459 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 17: After refmac, R = 0.1961 (Rfree = 0.000) for 1454 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2128 (Rfree = 0.000) for 1450 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.1995 (Rfree = 0.000) for 1445 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1959 (Rfree = 0.000) for 1442 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward NCS extension: 0 residues added, 1494 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 12 peptides. Score 0.294 Round 2: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.366 Round 3: 90 peptides, 13 chains. Longest chain 19 peptides. Score 0.482 Round 4: 89 peptides, 12 chains. Longest chain 25 peptides. Score 0.506 Round 5: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 4 Chains 12, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3514 restraints for refining 1459 atoms. 3218 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2133 (Rfree = 0.000) for 1459 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.1804 (Rfree = 0.000) for 1455 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.1916 (Rfree = 0.000) for 1454 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.1958 (Rfree = 0.000) for 1448 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2318 (Rfree = 0.000) for 1445 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 1483 seeds are put forward NCS extension: 48 residues added (0 deleted due to clashes), 1531 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.347 Round 2: 78 peptides, 11 chains. Longest chain 13 peptides. Score 0.461 Round 3: 80 peptides, 10 chains. Longest chain 14 peptides. Score 0.507 Round 4: 84 peptides, 10 chains. Longest chain 19 peptides. Score 0.533 Round 5: 88 peptides, 10 chains. Longest chain 15 peptides. Score 0.559 Taking the results from Round 5 Chains 10, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3415 restraints for refining 1459 atoms. 3113 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1860 (Rfree = 0.000) for 1459 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.1578 (Rfree = 0.000) for 1456 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.1445 (Rfree = 0.000) for 1451 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1500 (Rfree = 0.000) for 1448 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.1596 (Rfree = 0.000) for 1442 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 1487 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 1513 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 12 peptides. Score 0.294 Round 2: 81 peptides, 13 chains. Longest chain 17 peptides. Score 0.417 Round 3: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.336 Round 4: 80 peptides, 12 chains. Longest chain 12 peptides. Score 0.443 Round 5: 90 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Taking the results from Round 5 Chains 14, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3465 restraints for refining 1459 atoms. 3175 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1761 (Rfree = 0.000) for 1459 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.1552 (Rfree = 0.000) for 1451 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.1603 (Rfree = 0.000) for 1447 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1718 (Rfree = 0.000) for 1438 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1512 (Rfree = 0.000) for 1435 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 1476 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1491 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 13 peptides. Score 0.307 Round 2: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.422 Round 3: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.404 Round 4: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.379 Round 5: 84 peptides, 14 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 2 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3357 restraints for refining 1445 atoms. 3083 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1639 (Rfree = 0.000) for 1445 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.1521 (Rfree = 0.000) for 1437 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.1473 (Rfree = 0.000) for 1433 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1396 (Rfree = 0.000) for 1426 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1276 (Rfree = 0.000) for 1418 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 1458 seeds are put forward NCS extension: 0 residues added, 1458 seeds are put forward Round 1: 59 peptides, 14 chains. Longest chain 5 peptides. Score 0.195 Round 2: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.309 Round 3: 83 peptides, 14 chains. Longest chain 12 peptides. Score 0.399 Round 4: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.399 Round 5: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 5 Chains 15, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3511 restraints for refining 1459 atoms. 3234 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1736 (Rfree = 0.000) for 1459 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 42: After refmac, R = 0.1455 (Rfree = 0.000) for 1454 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1383 (Rfree = 0.000) for 1447 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1343 (Rfree = 0.000) for 1446 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1394 (Rfree = 0.000) for 1443 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 1481 seeds are put forward NCS extension: 0 residues added, 1481 seeds are put forward Round 1: 45 peptides, 11 chains. Longest chain 5 peptides. Score 0.177 Round 2: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.207 Round 3: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.251 Round 4: 39 peptides, 8 chains. Longest chain 8 peptides. Score 0.244 Round 5: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.229 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 35, 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 2od4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1758 reflections ( 98.27 % complete ) and 3692 restraints for refining 1447 atoms. 3561 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1472 (Rfree = 0.000) for 1447 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1437 (Rfree = 0.000) for 1444 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1486 (Rfree = 0.000) for 1441 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1277 (Rfree = 0.000) for 1437 atoms. TimeTaking 22.4