null Sun 23 Dec 22:22:53 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 1vk2-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.8-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/1vk2-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.8-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 22:23:03 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/1vk2-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.8-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: 0.6705 Checking the provided sequence file Detected sequence length: 204 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 204 Adjusted target solvent content: 0.54 Input MTZ file: 1vk2-3.8-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: 96 Cell parameters: 61.120 61.120 127.494 90.000 90.000 90.000 Input sequence file: 1vk2-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1632 target number of atoms Had to go as low as 0.80 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: 55.114 3.801 Wilson plot Bfac: 91.44 2659 reflections ( 99.77 % complete ) and 0 restraints for refining 1799 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3547 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3513 (Rfree = 0.000) for 1799 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 1828 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.326 Round 2: 96 peptides, 14 chains. Longest chain 15 peptides. Score 0.467 Round 3: 113 peptides, 16 chains. Longest chain 12 peptides. Score 0.517 Round 4: 106 peptides, 12 chains. Longest chain 13 peptides. Score 0.579 Round 5: 106 peptides, 15 chains. Longest chain 21 peptides. Score 0.502 Taking the results from Round 4 Chains 12, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 3517 restraints for refining 1476 atoms. 3153 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2865 (Rfree = 0.000) for 1476 atoms. Found 4 (8 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.3124 (Rfree = 0.000) for 1417 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.3368 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.3088 (Rfree = 0.000) for 1362 atoms. Found 2 (7 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.3114 (Rfree = 0.000) for 1335 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 1388 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.352 Round 2: 97 peptides, 13 chains. Longest chain 14 peptides. Score 0.501 Round 3: 97 peptides, 13 chains. Longest chain 17 peptides. Score 0.501 Round 4: 108 peptides, 12 chains. Longest chain 14 peptides. Score 0.589 Round 5: 103 peptides, 10 chains. Longest chain 21 peptides. Score 0.612 Taking the results from Round 5 Chains 10, Residues 93, Estimated correctness of the model 4.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 2924 restraints for refining 1287 atoms. 2562 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2936 (Rfree = 0.000) for 1287 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2820 (Rfree = 0.000) for 1274 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.2617 (Rfree = 0.000) for 1262 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2645 (Rfree = 0.000) for 1250 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2503 (Rfree = 0.000) for 1243 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 1312 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 11 peptides. Score 0.296 Round 2: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.419 Round 3: 96 peptides, 12 chains. Longest chain 17 peptides. Score 0.523 Round 4: 111 peptides, 13 chains. Longest chain 17 peptides. Score 0.581 Round 5: 102 peptides, 15 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 4 Chains 13, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 2683 restraints for refining 1287 atoms. 2304 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2651 (Rfree = 0.000) for 1287 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2590 (Rfree = 0.000) for 1269 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2466 (Rfree = 0.000) for 1263 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2522 (Rfree = 0.000) for 1257 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2662 (Rfree = 0.000) for 1251 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 1316 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 16 peptides. Score 0.352 Round 2: 113 peptides, 20 chains. Longest chain 14 peptides. Score 0.409 Round 3: 111 peptides, 18 chains. Longest chain 15 peptides. Score 0.451 Round 4: 107 peptides, 14 chains. Longest chain 15 peptides. Score 0.534 Round 5: 96 peptides, 14 chains. Longest chain 18 peptides. Score 0.467 Taking the results from Round 4 Chains 14, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 3032 restraints for refining 1373 atoms. 2674 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2791 (Rfree = 0.000) for 1373 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2427 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 18: After refmac, R = 0.2378 (Rfree = 0.000) for 1340 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.2265 (Rfree = 0.000) for 1336 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2285 (Rfree = 0.000) for 1332 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.326 Round 2: 107 peptides, 15 chains. Longest chain 20 peptides. Score 0.507 Round 3: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.428 Round 4: 97 peptides, 14 chains. Longest chain 16 peptides. Score 0.474 Round 5: 90 peptides, 12 chains. Longest chain 17 peptides. Score 0.486 Taking the results from Round 2 Chains 15, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 3085 restraints for refining 1392 atoms. 2732 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2499 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2265 (Rfree = 0.000) for 1384 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.2271 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2190 (Rfree = 0.000) for 1368 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 25: After refmac, R = 0.2275 (Rfree = 0.000) for 1353 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 21 peptides. Score 0.355 Round 2: 101 peptides, 17 chains. Longest chain 23 peptides. Score 0.415 Round 3: 100 peptides, 14 chains. Longest chain 23 peptides. Score 0.492 Round 4: 104 peptides, 15 chains. Longest chain 15 peptides. Score 0.489 Round 5: 105 peptides, 16 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 3 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 2968 restraints for refining 1373 atoms. 2638 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2172 (Rfree = 0.000) for 1373 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.1990 (Rfree = 0.000) for 1364 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2294 (Rfree = 0.000) for 1360 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2040 (Rfree = 0.000) for 1353 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2087 (Rfree = 0.000) for 1349 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.296 Round 2: 99 peptides, 17 chains. Longest chain 14 peptides. Score 0.401 Round 3: 102 peptides, 16 chains. Longest chain 15 peptides. Score 0.449 Round 4: 93 peptides, 14 chains. Longest chain 15 peptides. Score 0.448 Round 5: 98 peptides, 13 chains. Longest chain 13 peptides. Score 0.507 Taking the results from Round 5 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 3170 restraints for refining 1429 atoms. 2813 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2386 (Rfree = 0.000) for 1429 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 32: After refmac, R = 0.2136 (Rfree = 0.000) for 1413 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 33: After refmac, R = 0.2032 (Rfree = 0.000) for 1403 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.1981 (Rfree = 0.000) for 1398 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1956 (Rfree = 0.000) for 1394 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 1448 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.323 Round 2: 81 peptides, 13 chains. Longest chain 17 peptides. Score 0.397 Round 3: 86 peptides, 13 chains. Longest chain 19 peptides. Score 0.431 Round 4: 77 peptides, 11 chains. Longest chain 18 peptides. Score 0.432 Round 5: 87 peptides, 14 chains. Longest chain 19 peptides. Score 0.408 Taking the results from Round 4 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 3141 restraints for refining 1373 atoms. 2888 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2256 (Rfree = 0.000) for 1373 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 37: After refmac, R = 0.2123 (Rfree = 0.000) for 1366 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2507 (Rfree = 0.000) for 1366 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 39: After refmac, R = 0.2456 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.2053 (Rfree = 0.000) for 1347 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 9 peptides. Score 0.268 Round 2: 85 peptides, 14 chains. Longest chain 19 peptides. Score 0.395 Round 3: 89 peptides, 15 chains. Longest chain 16 peptides. Score 0.392 Round 4: 89 peptides, 15 chains. Longest chain 19 peptides. Score 0.392 Round 5: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 5 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2659 reflections ( 99.77 % complete ) and 3287 restraints for refining 1419 atoms. 3028 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2224 (Rfree = 0.000) for 1419 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2113 (Rfree = 0.000) for 1412 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1788 (Rfree = 0.000) for 1413 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.1822 (Rfree = 0.000) for 1410 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1706 (Rfree = 0.000) for 1406 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 1456 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.266 Round 2: 70 peptides, 10 chains. Longest chain 14 peptides. Score 0.415 Round 3: 79 peptides, 13 chains. Longest chain 13 peptides. Score 0.383 Round 4: 83 peptides, 14 chains. Longest chain 13 peptides. Score 0.381 Round 5: 85 peptides, 13 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 72, 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 1vk2-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2659 reflections ( 99.77 % complete ) and 3129 restraints for refining 1431 atoms. 2854 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2380 (Rfree = 0.000) for 1431 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2471 (Rfree = 0.000) for 1417 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2522 (Rfree = 0.000) for 1408 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2477 (Rfree = 0.000) for 1402 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:21 GMT 2018 Job finished. TimeTaking 28.48 Used memory is bytes: 11877240