null Sun 23 Dec 22:22:43 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.4-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 22:22:52 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-3.4-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 157 and 0 Target number of residues in the AU: 157 Target solvent content: 0.6182 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 60.55 3244 reflections ( 99.63 % complete ) and 0 restraints for refining 1736 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3334 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3305 (Rfree = 0.000) for 1736 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 1801 seeds are put forward Round 1: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.343 Round 2: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.422 Round 3: 102 peptides, 16 chains. Longest chain 13 peptides. Score 0.463 Round 4: 99 peptides, 15 chains. Longest chain 15 peptides. Score 0.472 Round 5: 108 peptides, 16 chains. Longest chain 13 peptides. Score 0.502 Taking the results from Round 5 Chains 16, Residues 92, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3230 restraints for refining 1433 atoms. 2850 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3021 (Rfree = 0.000) for 1433 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.3032 (Rfree = 0.000) for 1394 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2865 (Rfree = 0.000) for 1375 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2823 (Rfree = 0.000) for 1369 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2666 (Rfree = 0.000) for 1356 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1415 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.364 Round 2: 91 peptides, 14 chains. Longest chain 12 peptides. Score 0.448 Round 3: 103 peptides, 16 chains. Longest chain 13 peptides. Score 0.470 Round 4: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.491 Round 5: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.495 Taking the results from Round 5 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3085 restraints for refining 1372 atoms. 2763 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2621 (Rfree = 0.000) for 1372 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.2497 (Rfree = 0.000) for 1358 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2386 (Rfree = 0.000) for 1356 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2292 (Rfree = 0.000) for 1357 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2223 (Rfree = 0.000) for 1352 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.04 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.364 Round 2: 109 peptides, 17 chains. Longest chain 17 peptides. Score 0.480 Round 3: 108 peptides, 16 chains. Longest chain 21 peptides. Score 0.502 Round 4: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.508 Round 5: 110 peptides, 16 chains. Longest chain 16 peptides. Score 0.515 Taking the results from Round 5 Chains 16, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3203 restraints for refining 1416 atoms. 2843 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2986 (Rfree = 0.000) for 1416 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2650 (Rfree = 0.000) for 1399 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2394 (Rfree = 0.000) for 1391 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2386 (Rfree = 0.000) for 1388 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2308 (Rfree = 0.000) for 1382 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.07 Search for helices and strands: 0 residues in 0 chains, 1475 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 7 peptides. Score 0.324 Round 2: 95 peptides, 15 chains. Longest chain 9 peptides. Score 0.445 Round 3: 93 peptides, 13 chains. Longest chain 20 peptides. Score 0.491 Round 4: 100 peptides, 12 chains. Longest chain 17 peptides. Score 0.563 Round 5: 93 peptides, 13 chains. Longest chain 22 peptides. Score 0.491 Taking the results from Round 4 Chains 12, Residues 88, Estimated correctness of the model 16.1 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3029 restraints for refining 1433 atoms. 2630 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2411 (Rfree = 0.000) for 1433 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.2394 (Rfree = 0.000) for 1425 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2278 (Rfree = 0.000) for 1423 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2188 (Rfree = 0.000) for 1424 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2037 (Rfree = 0.000) for 1418 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 10 peptides. Score 0.322 Round 2: 99 peptides, 14 chains. Longest chain 16 peptides. Score 0.501 Round 3: 98 peptides, 14 chains. Longest chain 22 peptides. Score 0.495 Round 4: 110 peptides, 12 chains. Longest chain 26 peptides. Score 0.618 Round 5: 100 peptides, 15 chains. Longest chain 17 peptides. Score 0.479 Taking the results from Round 4 Chains 12, Residues 98, Estimated correctness of the model 34.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 2911 restraints for refining 1433 atoms. 2449 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2282 (Rfree = 0.000) for 1433 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 22: After refmac, R = 0.2080 (Rfree = 0.000) for 1417 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2012 (Rfree = 0.000) for 1408 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.1970 (Rfree = 0.000) for 1402 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1735 (Rfree = 0.000) for 1401 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1462 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 15 peptides. Score 0.396 Round 2: 106 peptides, 18 chains. Longest chain 17 peptides. Score 0.432 Round 3: 91 peptides, 14 chains. Longest chain 15 peptides. Score 0.448 Round 4: 96 peptides, 14 chains. Longest chain 18 peptides. Score 0.482 Round 5: 99 peptides, 16 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 4 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3154 restraints for refining 1433 atoms. 2806 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2399 (Rfree = 0.000) for 1433 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.2066 (Rfree = 0.000) for 1430 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2025 (Rfree = 0.000) for 1425 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1956 (Rfree = 0.000) for 1421 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1968 (Rfree = 0.000) for 1421 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.10 Search for helices and strands: 0 residues in 0 chains, 1500 seeds are put forward Round 1: 92 peptides, 17 chains. Longest chain 16 peptides. Score 0.362 Round 2: 103 peptides, 14 chains. Longest chain 23 peptides. Score 0.526 Round 3: 83 peptides, 12 chains. Longest chain 25 peptides. Score 0.454 Round 4: 89 peptides, 12 chains. Longest chain 26 peptides. Score 0.494 Round 5: 99 peptides, 13 chains. Longest chain 27 peptides. Score 0.529 Taking the results from Round 5 Chains 13, Residues 86, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3211 restraints for refining 1433 atoms. 2880 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2320 (Rfree = 0.000) for 1433 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.1983 (Rfree = 0.000) for 1427 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.1888 (Rfree = 0.000) for 1425 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1781 (Rfree = 0.000) for 1427 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1745 (Rfree = 0.000) for 1421 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 19 peptides. Score 0.364 Round 2: 94 peptides, 14 chains. Longest chain 27 peptides. Score 0.468 Round 3: 98 peptides, 14 chains. Longest chain 16 peptides. Score 0.495 Round 4: 103 peptides, 16 chains. Longest chain 21 peptides. Score 0.470 Round 5: 103 peptides, 16 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 3 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3279 restraints for refining 1433 atoms. 2957 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2119 (Rfree = 0.000) for 1433 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2047 (Rfree = 0.000) for 1437 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2028 (Rfree = 0.000) for 1440 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.1953 (Rfree = 0.000) for 1442 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1851 (Rfree = 0.000) for 1441 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.05 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 76 peptides, 12 chains. Longest chain 16 peptides. Score 0.404 Round 2: 82 peptides, 11 chains. Longest chain 26 peptides. Score 0.478 Round 3: 78 peptides, 13 chains. Longest chain 13 peptides. Score 0.386 Round 4: 77 peptides, 11 chains. Longest chain 16 peptides. Score 0.444 Round 5: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 2 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3244 reflections ( 99.63 % complete ) and 3305 restraints for refining 1424 atoms. 3032 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2077 (Rfree = 0.000) for 1424 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.1917 (Rfree = 0.000) for 1426 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.1858 (Rfree = 0.000) for 1428 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.1804 (Rfree = 0.000) for 1428 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1578 (Rfree = 0.000) for 1428 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1482 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Round 2: 91 peptides, 15 chains. Longest chain 15 peptides. Score 0.417 Round 3: 81 peptides, 15 chains. Longest chain 12 peptides. Score 0.343 Round 4: 77 peptides, 12 chains. Longest chain 15 peptides. Score 0.412 Round 5: 83 peptides, 13 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 70, 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. 3244 reflections ( 99.63 % complete ) and 3275 restraints for refining 1431 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2126 (Rfree = 0.000) for 1431 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2183 (Rfree = 0.000) for 1422 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2176 (Rfree = 0.000) for 1415 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2021 (Rfree = 0.000) for 1404 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:55 GMT 2018 Job finished. TimeTaking 32.2 Used memory is bytes: 14954792