Mon 24 Dec 01:01:41 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 2ooc-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ooc-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-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/2ooc-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-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 01:01:45 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/2ooc-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ooc-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 153 and 0 Target number of residues in the AU: 153 Target solvent content: 0.6825 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.53 Input MTZ file: 2ooc-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: 154 Cell parameters: 62.597 62.597 115.277 90.000 90.000 120.000 Input sequence file: 2ooc-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1808 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: 54.211 4.000 Wilson plot Bfac: 102.83 2434 reflections ( 99.67 % complete ) and 0 restraints for refining 1990 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3562 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3413 (Rfree = 0.000) for 1990 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.96 3.80 Search for helices and strands: 0 residues in 0 chains, 2041 seeds are put forward NCS extension: 0 residues added, 2041 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.286 Round 2: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.389 Round 3: 95 peptides, 11 chains. Longest chain 17 peptides. Score 0.521 Round 4: 89 peptides, 10 chains. Longest chain 13 peptides. Score 0.514 Round 5: 95 peptides, 10 chains. Longest chain 14 peptides. Score 0.546 Taking the results from Round 5 Chains 10, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3845 restraints for refining 1593 atoms. 3515 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2585 (Rfree = 0.000) for 1593 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 2: After refmac, R = 0.2899 (Rfree = 0.000) for 1560 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 3: After refmac, R = 0.2679 (Rfree = 0.000) for 1522 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 4: After refmac, R = 0.2713 (Rfree = 0.000) for 1495 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2507 (Rfree = 0.000) for 1480 atoms. Found 0 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.91 3.76 Search for helices and strands: 0 residues in 0 chains, 1557 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1574 seeds are put forward Round 1: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.352 Round 2: 91 peptides, 11 chains. Longest chain 17 peptides. Score 0.498 Round 3: 100 peptides, 14 chains. Longest chain 12 peptides. Score 0.471 Round 4: 102 peptides, 12 chains. Longest chain 20 peptides. Score 0.533 Round 5: 103 peptides, 12 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 12, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3396 restraints for refining 1461 atoms. 3044 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2659 (Rfree = 0.000) for 1461 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.2454 (Rfree = 0.000) for 1440 atoms. Found 4 (6 requested) and removed 14 (3 requested) atoms. Cycle 8: After refmac, R = 0.2444 (Rfree = 0.000) for 1417 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 9: After refmac, R = 0.2480 (Rfree = 0.000) for 1400 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2548 (Rfree = 0.000) for 1391 atoms. Found 4 (6 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 1478 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1495 seeds are put forward Round 1: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.340 Round 2: 100 peptides, 12 chains. Longest chain 20 peptides. Score 0.522 Round 3: 99 peptides, 12 chains. Longest chain 19 peptides. Score 0.517 Round 4: 87 peptides, 11 chains. Longest chain 18 peptides. Score 0.476 Round 5: 98 peptides, 13 chains. Longest chain 19 peptides. Score 0.486 Taking the results from Round 2 Chains 13, Residues 88, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3024 restraints for refining 1442 atoms. 2634 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2514 (Rfree = 0.000) for 1442 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 12: After refmac, R = 0.2453 (Rfree = 0.000) for 1415 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 13: After refmac, R = 0.2412 (Rfree = 0.000) for 1390 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 14: After refmac, R = 0.2261 (Rfree = 0.000) for 1374 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 15: After refmac, R = 0.2207 (Rfree = 0.000) for 1359 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.97 3.81 Search for helices and strands: 0 residues in 0 chains, 1443 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1457 seeds are put forward Round 1: 93 peptides, 17 chains. Longest chain 12 peptides. Score 0.347 Round 2: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.448 Round 3: 92 peptides, 13 chains. Longest chain 12 peptides. Score 0.451 Round 4: 90 peptides, 12 chains. Longest chain 20 peptides. Score 0.466 Round 5: 95 peptides, 12 chains. Longest chain 12 peptides. Score 0.495 Taking the results from Round 5 Chains 12, Residues 83, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3384 restraints for refining 1513 atoms. 3024 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2662 (Rfree = 0.000) for 1513 atoms. Found 7 (7 requested) and removed 25 (3 requested) atoms. Cycle 17: After refmac, R = 0.2335 (Rfree = 0.000) for 1482 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2291 (Rfree = 0.000) for 1472 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2205 (Rfree = 0.000) for 1458 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2467 (Rfree = 0.000) for 1454 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.70 Search for helices and strands: 0 residues in 0 chains, 1538 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1554 seeds are put forward Round 1: 76 peptides, 12 chains. Longest chain 16 peptides. Score 0.379 Round 2: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.373 Round 3: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Round 4: 94 peptides, 14 chains. Longest chain 14 peptides. Score 0.436 Round 5: 89 peptides, 13 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 3 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3356 restraints for refining 1471 atoms. 3053 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2896 (Rfree = 0.000) for 1471 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 22: After refmac, R = 0.2578 (Rfree = 0.000) for 1435 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 23: After refmac, R = 0.2374 (Rfree = 0.000) for 1418 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 24: After refmac, R = 0.2379 (Rfree = 0.000) for 1404 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 25: After refmac, R = 0.2215 (Rfree = 0.000) for 1391 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.93 3.78 Search for helices and strands: 0 residues in 0 chains, 1521 seeds are put forward NCS extension: 0 residues added, 1521 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.293 Round 2: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.399 Round 3: 83 peptides, 12 chains. Longest chain 19 peptides. Score 0.424 Round 4: 88 peptides, 11 chains. Longest chain 19 peptides. Score 0.481 Round 5: 99 peptides, 14 chains. Longest chain 19 peptides. Score 0.466 Taking the results from Round 4 Chains 11, Residues 77, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3288 restraints for refining 1483 atoms. 2974 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2849 (Rfree = 0.000) for 1483 atoms. Found 7 (7 requested) and removed 29 (3 requested) atoms. Cycle 27: After refmac, R = 0.2501 (Rfree = 0.000) for 1446 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2444 (Rfree = 0.000) for 1436 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 29: After refmac, R = 0.2804 (Rfree = 0.000) for 1418 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 30: After refmac, R = 0.2647 (Rfree = 0.000) for 1404 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.74 Search for helices and strands: 0 residues in 0 chains, 1513 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 1532 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.248 Round 2: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.399 Round 3: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.347 Round 4: 74 peptides, 12 chains. Longest chain 15 peptides. Score 0.366 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 2 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3154 restraints for refining 1413 atoms. 2898 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2929 (Rfree = 0.000) for 1413 atoms. Found 6 (6 requested) and removed 29 (3 requested) atoms. Cycle 32: After refmac, R = 0.2682 (Rfree = 0.000) for 1381 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.2856 (Rfree = 0.000) for 1371 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 34: After refmac, R = 0.3002 (Rfree = 0.000) for 1360 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 35: After refmac, R = 0.2623 (Rfree = 0.000) for 1352 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1464 seeds are put forward Round 1: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.352 Round 2: 72 peptides, 12 chains. Longest chain 13 peptides. Score 0.352 Round 3: 72 peptides, 11 chains. Longest chain 14 peptides. Score 0.382 Round 4: 74 peptides, 13 chains. Longest chain 8 peptides. Score 0.336 Round 5: 90 peptides, 14 chains. Longest chain 11 peptides. Score 0.411 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 ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3222 restraints for refining 1438 atoms. 2932 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2713 (Rfree = 0.000) for 1438 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 37: After refmac, R = 0.2946 (Rfree = 0.000) for 1409 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 38: After refmac, R = 0.2898 (Rfree = 0.000) for 1400 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 39: After refmac, R = 0.2854 (Rfree = 0.000) for 1381 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 40: After refmac, R = 0.2737 (Rfree = 0.000) for 1372 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 3.73 Search for helices and strands: 0 residues in 0 chains, 1459 seeds are put forward NCS extension: 0 residues added, 1459 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 8 peptides. Score 0.227 Round 2: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.393 Round 3: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.448 Round 4: 94 peptides, 12 chains. Longest chain 14 peptides. Score 0.489 Round 5: 91 peptides, 12 chains. Longest chain 16 peptides. Score 0.472 Taking the results from Round 4 Chains 12, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2434 reflections ( 99.67 % complete ) and 3175 restraints for refining 1440 atoms. 2859 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3218 (Rfree = 0.000) for 1440 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 42: After refmac, R = 0.2690 (Rfree = 0.000) for 1424 atoms. Found 4 (6 requested) and removed 14 (3 requested) atoms. Cycle 43: After refmac, R = 0.2371 (Rfree = 0.000) for 1409 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 44: After refmac, R = 0.2440 (Rfree = 0.000) for 1402 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2246 (Rfree = 0.000) for 1399 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.70 Search for helices and strands: 0 residues in 0 chains, 1468 seeds are put forward NCS extension: 0 residues added, 1468 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.222 Round 2: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.340 Round 3: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.373 Round 4: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.371 Round 5: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 67, 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 2ooc-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2434 reflections ( 99.67 % complete ) and 3660 restraints for refining 1558 atoms. 3405 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2946 (Rfree = 0.000) for 1558 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2275 (Rfree = 0.000) for 1543 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2849 (Rfree = 0.000) for 1530 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2403 (Rfree = 0.000) for 1517 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 20.72