Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ooc-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooc-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-3.8-parrot-hancs ############### 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 22:22:54 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/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooc-3.8-parrot-hancs/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 160 and 0 Target number of residues in the AU: 160 Target solvent content: 0.6680 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-3.8-parrot-hancs.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-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 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: 54.211 3.801 Wilson plot Bfac: 90.84 2820 reflections ( 99.72 % complete ) and 0 restraints for refining 2001 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3549 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3275 (Rfree = 0.000) for 2001 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 2064 seeds are put forward NCS extension: 0 residues added, 2064 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.344 Round 2: 92 peptides, 13 chains. Longest chain 11 peptides. Score 0.451 Round 3: 96 peptides, 13 chains. Longest chain 11 peptides. Score 0.474 Round 4: 98 peptides, 13 chains. Longest chain 14 peptides. Score 0.486 Round 5: 104 peptides, 13 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 13, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 4030 restraints for refining 1635 atoms. 3679 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2356 (Rfree = 0.000) for 1635 atoms. Found 4 (8 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2437 (Rfree = 0.000) for 1589 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2308 (Rfree = 0.000) for 1548 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 4: After refmac, R = 0.2386 (Rfree = 0.000) for 1514 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2240 (Rfree = 0.000) for 1498 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 1603 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 1632 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.315 Round 2: 97 peptides, 14 chains. Longest chain 12 peptides. Score 0.454 Round 3: 97 peptides, 15 chains. Longest chain 12 peptides. Score 0.427 Round 4: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.457 Round 5: 108 peptides, 14 chains. Longest chain 14 peptides. Score 0.516 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 ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3264 restraints for refining 1440 atoms. 2902 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2343 (Rfree = 0.000) for 1440 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 7: After refmac, R = 0.2271 (Rfree = 0.000) for 1415 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.2309 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2281 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 10: After refmac, R = 0.2298 (Rfree = 0.000) for 1384 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 1454 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1471 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.320 Round 2: 98 peptides, 14 chains. Longest chain 14 peptides. Score 0.460 Round 3: 98 peptides, 14 chains. Longest chain 14 peptides. Score 0.460 Round 4: 102 peptides, 14 chains. Longest chain 16 peptides. Score 0.483 Round 5: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 4 Chains 14, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3399 restraints for refining 1495 atoms. 3061 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2275 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.2288 (Rfree = 0.000) for 1476 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 1452 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2279 (Rfree = 0.000) for 1438 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2159 (Rfree = 0.000) for 1426 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward NCS extension: 0 residues added, 1515 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.296 Round 2: 88 peptides, 14 chains. Longest chain 11 peptides. Score 0.399 Round 3: 91 peptides, 13 chains. Longest chain 20 peptides. Score 0.445 Round 4: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.408 Round 5: 92 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3324 restraints for refining 1484 atoms. 2981 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2310 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 23 (4 requested) atoms. Cycle 17: After refmac, R = 0.2482 (Rfree = 0.000) for 1447 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 18: After refmac, R = 0.2434 (Rfree = 0.000) for 1412 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 19: After refmac, R = 0.2275 (Rfree = 0.000) for 1397 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 20: After refmac, R = 0.2373 (Rfree = 0.000) for 1389 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 1482 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1490 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 11 peptides. Score 0.300 Round 2: 92 peptides, 14 chains. Longest chain 11 peptides. Score 0.424 Round 3: 99 peptides, 15 chains. Longest chain 11 peptides. Score 0.439 Round 4: 96 peptides, 15 chains. Longest chain 14 peptides. Score 0.421 Round 5: 88 peptides, 14 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 3 Chains 15, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3184 restraints for refining 1421 atoms. 2863 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2376 (Rfree = 0.000) for 1421 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 22: After refmac, R = 0.2358 (Rfree = 0.000) for 1397 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 23: After refmac, R = 0.2196 (Rfree = 0.000) for 1381 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.2338 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 25: After refmac, R = 0.2346 (Rfree = 0.000) for 1366 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 1466 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1478 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.256 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.322 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.355 Round 4: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.360 Round 5: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 5 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3200 restraints for refining 1429 atoms. 2897 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2582 (Rfree = 0.000) for 1429 atoms. Found 7 (7 requested) and removed 24 (3 requested) atoms. Cycle 27: After refmac, R = 0.2629 (Rfree = 0.000) for 1400 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 28: After refmac, R = 0.2348 (Rfree = 0.000) for 1390 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 29: After refmac, R = 0.2406 (Rfree = 0.000) for 1379 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2337 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 1463 seeds are put forward NCS extension: 0 residues added, 1463 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.244 Round 2: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.364 Round 3: 86 peptides, 14 chains. Longest chain 11 peptides. Score 0.386 Round 4: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.399 Round 5: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 4 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3205 restraints for refining 1397 atoms. 2923 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2619 (Rfree = 0.000) for 1397 atoms. Found 7 (7 requested) and removed 21 (3 requested) atoms. Cycle 32: After refmac, R = 0.2298 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 33: After refmac, R = 0.2499 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.2375 (Rfree = 0.000) for 1357 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 35: After refmac, R = 0.2252 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.46 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: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.308 Round 2: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.317 Round 3: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.355 Round 4: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.403 Round 5: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 4 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 3030 restraints for refining 1411 atoms. 2681 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2428 (Rfree = 0.000) for 1411 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 37: After refmac, R = 0.2102 (Rfree = 0.000) for 1394 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 38: After refmac, R = 0.2306 (Rfree = 0.000) for 1378 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.1827 (Rfree = 0.000) for 1369 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2214 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 1417 seeds are put forward NCS extension: 0 residues added, 1417 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.313 Round 2: 70 peptides, 10 chains. Longest chain 13 peptides. Score 0.399 Round 3: 70 peptides, 12 chains. Longest chain 13 peptides. Score 0.338 Round 4: 71 peptides, 11 chains. Longest chain 9 peptides. Score 0.376 Round 5: 75 peptides, 12 chains. Longest chain 14 peptides. Score 0.372 Taking the results from Round 2 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 2820 reflections ( 99.72 % complete ) and 2969 restraints for refining 1374 atoms. 2662 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2360 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.2390 (Rfree = 0.000) for 1363 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 43: After refmac, R = 0.2475 (Rfree = 0.000) for 1348 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.2340 (Rfree = 0.000) for 1340 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2430 (Rfree = 0.000) for 1334 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward NCS extension: 0 residues added, 1404 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.234 Round 2: 66 peptides, 13 chains. Longest chain 9 peptides. Score 0.278 Round 3: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.338 Round 4: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.338 Round 5: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.291 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 51, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2820 reflections ( 99.72 % complete ) and 2938 restraints for refining 1303 atoms. 2744 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2819 (Rfree = 0.000) for 1303 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2415 (Rfree = 0.000) for 1291 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2498 (Rfree = 0.000) for 1282 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2353 (Rfree = 0.000) for 1275 atoms. TimeTaking 29.13