null Mon 24 Dec 07:28:16 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 2od4-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od4-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od4-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.6-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/2od4-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.6-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 07:28:20 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/2od4-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-3.6-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6402 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: 2od4-3.6-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 1616 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: 28.889 3.600 Wilson plot Bfac: 70.75 2426 reflections ( 98.42 % complete ) and 0 restraints for refining 1785 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3163 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2937 (Rfree = 0.000) for 1785 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 0 residues added, 1821 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.242 Round 2: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.422 Round 3: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.392 Round 4: 105 peptides, 15 chains. Longest chain 14 peptides. Score 0.523 Round 5: 106 peptides, 14 chains. Longest chain 15 peptides. Score 0.557 Taking the results from Round 5 Chains 14, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3326 restraints for refining 1464 atoms. 2972 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2267 (Rfree = 0.000) for 1464 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 2: After refmac, R = 0.2262 (Rfree = 0.000) for 1449 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2191 (Rfree = 0.000) for 1442 atoms. Found 7 (9 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2044 (Rfree = 0.000) for 1436 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.1727 (Rfree = 0.000) for 1431 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 1486 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1508 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.346 Round 2: 86 peptides, 14 chains. Longest chain 10 peptides. Score 0.422 Round 3: 81 peptides, 12 chains. Longest chain 15 peptides. Score 0.450 Round 4: 84 peptides, 11 chains. Longest chain 17 peptides. Score 0.503 Round 5: 84 peptides, 13 chains. Longest chain 22 peptides. Score 0.439 Taking the results from Round 4 Chains 11, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3451 restraints for refining 1461 atoms. 3170 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1979 (Rfree = 0.000) for 1461 atoms. Found 8 (9 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.1845 (Rfree = 0.000) for 1450 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2324 (Rfree = 0.000) for 1446 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 9: After refmac, R = 0.2100 (Rfree = 0.000) for 1434 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2030 (Rfree = 0.000) for 1429 atoms. Found 6 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 1474 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 1510 seeds are put forward Round 1: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.352 Round 2: 76 peptides, 12 chains. Longest chain 13 peptides. Score 0.413 Round 3: 92 peptides, 14 chains. Longest chain 17 peptides. Score 0.465 Round 4: 89 peptides, 13 chains. Longest chain 13 peptides. Score 0.475 Round 5: 91 peptides, 13 chains. Longest chain 18 peptides. Score 0.489 Taking the results from Round 5 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3461 restraints for refining 1465 atoms. 3162 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2034 (Rfree = 0.000) for 1465 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.1929 (Rfree = 0.000) for 1452 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.1485 (Rfree = 0.000) for 1449 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.1635 (Rfree = 0.000) for 1441 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.1718 (Rfree = 0.000) for 1435 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 1489 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 1522 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 7 peptides. Score 0.230 Round 2: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.389 Round 3: 83 peptides, 13 chains. Longest chain 16 peptides. Score 0.432 Round 4: 94 peptides, 15 chains. Longest chain 16 peptides. Score 0.448 Round 5: 102 peptides, 13 chains. Longest chain 20 peptides. Score 0.560 Taking the results from Round 5 Chains 13, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3280 restraints for refining 1465 atoms. 2937 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1686 (Rfree = 0.000) for 1465 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.1649 (Rfree = 0.000) for 1453 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.1614 (Rfree = 0.000) for 1452 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2190 (Rfree = 0.000) for 1448 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 20: After refmac, R = 0.1450 (Rfree = 0.000) for 1430 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 1492 seeds are put forward NCS extension: 0 residues added, 1492 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.303 Round 2: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.414 Round 3: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.379 Round 4: 90 peptides, 15 chains. Longest chain 12 peptides. Score 0.419 Round 5: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3377 restraints for refining 1465 atoms. 3099 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1721 (Rfree = 0.000) for 1465 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 22: After refmac, R = 0.1536 (Rfree = 0.000) for 1461 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.1430 (Rfree = 0.000) for 1456 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.1426 (Rfree = 0.000) for 1450 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1400 (Rfree = 0.000) for 1446 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 0 residues added, 1485 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.249 Round 2: 76 peptides, 13 chains. Longest chain 13 peptides. Score 0.379 Round 3: 86 peptides, 12 chains. Longest chain 13 peptides. Score 0.485 Round 4: 82 peptides, 12 chains. Longest chain 9 peptides. Score 0.457 Round 5: 94 peptides, 14 chains. Longest chain 13 peptides. Score 0.479 Taking the results from Round 3 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3345 restraints for refining 1465 atoms. 3061 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1593 (Rfree = 0.000) for 1465 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 27: After refmac, R = 0.1460 (Rfree = 0.000) for 1461 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.1409 (Rfree = 0.000) for 1457 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.1395 (Rfree = 0.000) for 1452 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1375 (Rfree = 0.000) for 1448 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 1486 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1507 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 6 peptides. Score 0.272 Round 2: 92 peptides, 14 chains. Longest chain 10 peptides. Score 0.465 Round 3: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.472 Round 4: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.431 Round 5: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.409 Taking the results from Round 3 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3350 restraints for refining 1465 atoms. 3048 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1664 (Rfree = 0.000) for 1465 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.1382 (Rfree = 0.000) for 1465 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1503 (Rfree = 0.000) for 1459 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.1336 (Rfree = 0.000) for 1457 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1406 (Rfree = 0.000) for 1454 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 0 residues added, 1485 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.279 Round 2: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.360 Round 3: 87 peptides, 14 chains. Longest chain 9 peptides. Score 0.429 Round 4: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.402 Round 5: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.405 Taking the results from Round 3 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3407 restraints for refining 1465 atoms. 3129 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1708 (Rfree = 0.000) for 1465 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 37: After refmac, R = 0.1941 (Rfree = 0.000) for 1463 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.1644 (Rfree = 0.000) for 1465 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.1744 (Rfree = 0.000) for 1465 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.1694 (Rfree = 0.000) for 1467 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 1516 seeds are put forward NCS extension: 0 residues added, 1516 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.279 Round 2: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.360 Round 3: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.330 Round 4: 74 peptides, 14 chains. Longest chain 7 peptides. Score 0.328 Round 5: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 5 Chains 13, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3434 restraints for refining 1465 atoms. 3199 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2117 (Rfree = 0.000) for 1465 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2117 (Rfree = 0.000) for 1461 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.2052 (Rfree = 0.000) for 1457 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.1961 (Rfree = 0.000) for 1453 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.1871 (Rfree = 0.000) for 1455 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 1498 seeds are put forward NCS extension: 0 residues added, 1498 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.196 Round 2: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.275 Round 3: 72 peptides, 15 chains. Longest chain 9 peptides. Score 0.275 Round 4: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.349 Round 5: 71 peptides, 13 chains. Longest chain 11 peptides. Score 0.338 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 56, 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 2od4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2426 reflections ( 98.42 % complete ) and 3422 restraints for refining 1442 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1889 (Rfree = 0.000) for 1442 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1785 (Rfree = 0.000) for 1433 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1889 (Rfree = 0.000) for 1426 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1732 (Rfree = 0.000) for 1419 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:48:51 GMT 2018 Job finished. TimeTaking 20.59 Used memory is bytes: 1400232