null Sun 23 Dec 22:22:41 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 2hyt-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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/2hyt-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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 22:22:50 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/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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 145 and 0 Target number of residues in the AU: 145 Target solvent content: 0.6474 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 197 Adjusted target solvent content: 0.52 Input MTZ file: 2hyt-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: 150 Cell parameters: 82.957 82.957 56.010 90.000 90.000 120.000 Input sequence file: 2hyt-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1576 target number of atoms Had to go as low as 0.90 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 Loops will be built when appropriate and at the last cycle Resolution range: 71.843 3.801 Wilson plot Bfac: 76.52 2331 reflections ( 99.49 % complete ) and 0 restraints for refining 1740 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3469 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3271 (Rfree = 0.000) for 1740 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 1797 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.233 Round 2: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.334 Round 3: 106 peptides, 15 chains. Longest chain 24 peptides. Score 0.517 Round 4: 104 peptides, 13 chains. Longest chain 18 peptides. Score 0.559 Round 5: 102 peptides, 14 chains. Longest chain 16 peptides. Score 0.520 Taking the results from Round 4 Chains 14, Residues 91, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3188 restraints for refining 1423 atoms. 2811 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2596 (Rfree = 0.000) for 1423 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2507 (Rfree = 0.000) for 1390 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2585 (Rfree = 0.000) for 1372 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2340 (Rfree = 0.000) for 1361 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2141 (Rfree = 0.000) for 1352 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 1441 seeds are put forward Round 1: 82 peptides, 14 chains. Longest chain 12 peptides. Score 0.384 Round 2: 92 peptides, 13 chains. Longest chain 18 peptides. Score 0.485 Round 3: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.445 Round 4: 100 peptides, 13 chains. Longest chain 23 peptides. Score 0.535 Round 5: 104 peptides, 15 chains. Longest chain 10 peptides. Score 0.505 Taking the results from Round 4 Chains 15, Residues 87, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3188 restraints for refining 1425 atoms. 2801 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2447 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.2100 (Rfree = 0.000) for 1406 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 8: After refmac, R = 0.2034 (Rfree = 0.000) for 1399 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2024 (Rfree = 0.000) for 1402 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.2019 (Rfree = 0.000) for 1404 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 1458 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.316 Round 2: 97 peptides, 15 chains. Longest chain 16 peptides. Score 0.459 Round 3: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.479 Round 4: 104 peptides, 13 chains. Longest chain 16 peptides. Score 0.559 Round 5: 103 peptides, 16 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 4 Chains 14, Residues 91, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3094 restraints for refining 1425 atoms. 2682 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2435 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 12: After refmac, R = 0.2718 (Rfree = 0.000) for 1409 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2329 (Rfree = 0.000) for 1404 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.2361 (Rfree = 0.000) for 1405 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 15: After refmac, R = 0.2246 (Rfree = 0.000) for 1399 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1462 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 5 peptides. Score 0.226 Round 2: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.406 Round 3: 85 peptides, 13 chains. Longest chain 10 peptides. Score 0.437 Round 4: 85 peptides, 12 chains. Longest chain 11 peptides. Score 0.468 Round 5: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.351 Taking the results from Round 4 Chains 12, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3456 restraints for refining 1425 atoms. 3176 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2540 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 17: After refmac, R = 0.2455 (Rfree = 0.000) for 1418 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2353 (Rfree = 0.000) for 1413 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2314 (Rfree = 0.000) for 1413 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1869 (Rfree = 0.000) for 1408 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1475 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 12 peptides. Score 0.304 Round 2: 84 peptides, 13 chains. Longest chain 12 peptides. Score 0.430 Round 3: 80 peptides, 11 chains. Longest chain 12 peptides. Score 0.465 Round 4: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.406 Round 5: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 3 Chains 11, Residues 69, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3441 restraints for refining 1425 atoms. 3155 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2409 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.2195 (Rfree = 0.000) for 1421 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.1952 (Rfree = 0.000) for 1418 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1655 (Rfree = 0.000) for 1416 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1661 (Rfree = 0.000) for 1415 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 1482 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.286 Round 2: 78 peptides, 11 chains. Longest chain 15 peptides. Score 0.451 Round 3: 78 peptides, 12 chains. Longest chain 16 peptides. Score 0.419 Round 4: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.369 Round 5: 79 peptides, 12 chains. Longest chain 16 peptides. Score 0.426 Taking the results from Round 2 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3467 restraints for refining 1424 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2144 (Rfree = 0.000) for 1424 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 27: After refmac, R = 0.1975 (Rfree = 0.000) for 1413 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.1730 (Rfree = 0.000) for 1412 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1669 (Rfree = 0.000) for 1413 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1961 (Rfree = 0.000) for 1411 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 1473 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.239 Round 2: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.316 Round 3: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.351 Round 4: 67 peptides, 13 chains. Longest chain 10 peptides. Score 0.300 Round 5: 74 peptides, 12 chains. Longest chain 13 peptides. Score 0.389 Taking the results from Round 5 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3430 restraints for refining 1424 atoms. 3194 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2728 (Rfree = 0.000) for 1424 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 32: After refmac, R = 0.2354 (Rfree = 0.000) for 1418 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2265 (Rfree = 0.000) for 1415 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2094 (Rfree = 0.000) for 1410 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2010 (Rfree = 0.000) for 1410 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 1453 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.213 Round 2: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.330 Round 3: 70 peptides, 13 chains. Longest chain 10 peptides. Score 0.324 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.351 Round 5: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 4 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3414 restraints for refining 1424 atoms. 3161 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2504 (Rfree = 0.000) for 1424 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2268 (Rfree = 0.000) for 1408 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.1811 (Rfree = 0.000) for 1400 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.1630 (Rfree = 0.000) for 1396 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1634 (Rfree = 0.000) for 1392 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1450 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 5 peptides. Score 0.215 Round 2: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.305 Round 3: 60 peptides, 10 chains. Longest chain 8 peptides. Score 0.349 Round 4: 66 peptides, 11 chains. Longest chain 8 peptides. Score 0.362 Round 5: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.312 Taking the results from Round 4 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2331 reflections ( 99.49 % complete ) and 3394 restraints for refining 1424 atoms. 3185 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2252 (Rfree = 0.000) for 1424 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 42: After refmac, R = 0.2291 (Rfree = 0.000) for 1416 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2153 (Rfree = 0.000) for 1415 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2162 (Rfree = 0.000) for 1409 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2085 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1461 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.196 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.275 Round 3: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.319 Round 4: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.304 Round 5: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 54, 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 2hyt-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2331 reflections ( 99.49 % complete ) and 3319 restraints for refining 1400 atoms. 3115 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2439 (Rfree = 0.000) for 1400 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2567 (Rfree = 0.000) for 1383 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2502 (Rfree = 0.000) for 1372 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2381 (Rfree = 0.000) for 1364 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:10 GMT 2018 Job finished. TimeTaking 31.49 Used memory is bytes: 13273944