Sun 23 Dec 22:23:05 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 1vk2-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-4.0-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/1vk2-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-4.0-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 22:23:15 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/1vk2-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-4.0-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6796 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: 1vk2-4.0-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: 1vk2-4.0-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 4.001 Wilson plot Bfac: 99.28 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2308 reflections ( 99.78 % complete ) and 0 restraints for refining 1796 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3568 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3562 (Rfree = 0.000) for 1796 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.89 3.69 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 14 peptides. Score 0.362 Round 2: 98 peptides, 13 chains. Longest chain 17 peptides. Score 0.507 Round 3: 99 peptides, 13 chains. Longest chain 13 peptides. Score 0.513 Round 4: 94 peptides, 12 chains. Longest chain 16 peptides. Score 0.511 Round 5: 109 peptides, 14 chains. Longest chain 14 peptides. Score 0.545 Taking the results from Round 5 Chains 14, Residues 95, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 3375 restraints for refining 1472 atoms. 2976 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2992 (Rfree = 0.000) for 1472 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 2: After refmac, R = 0.3019 (Rfree = 0.000) for 1423 atoms. Found 5 (6 requested) and removed 16 (3 requested) atoms. Cycle 3: After refmac, R = 0.2810 (Rfree = 0.000) for 1390 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 4: After refmac, R = 0.2828 (Rfree = 0.000) for 1368 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 5: After refmac, R = 0.2783 (Rfree = 0.000) for 1347 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 1414 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 10 peptides. Score 0.308 Round 2: 100 peptides, 13 chains. Longest chain 15 peptides. Score 0.519 Round 3: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.477 Round 4: 101 peptides, 11 chains. Longest chain 24 peptides. Score 0.577 Round 5: 99 peptides, 13 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 4 Chains 12, Residues 90, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 3236 restraints for refining 1453 atoms. 2839 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2933 (Rfree = 0.000) for 1453 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 7: After refmac, R = 0.2768 (Rfree = 0.000) for 1407 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 8: After refmac, R = 0.2495 (Rfree = 0.000) for 1383 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 9: After refmac, R = 0.2716 (Rfree = 0.000) for 1372 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 10: After refmac, R = 0.2476 (Rfree = 0.000) for 1356 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.308 Round 2: 97 peptides, 15 chains. Longest chain 12 peptides. Score 0.446 Round 3: 99 peptides, 13 chains. Longest chain 17 peptides. Score 0.513 Round 4: 94 peptides, 13 chains. Longest chain 15 peptides. Score 0.483 Round 5: 103 peptides, 13 chains. Longest chain 16 peptides. Score 0.537 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 3033 restraints for refining 1378 atoms. 2686 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2900 (Rfree = 0.000) for 1378 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2972 (Rfree = 0.000) for 1356 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 13: After refmac, R = 0.2778 (Rfree = 0.000) for 1339 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2828 (Rfree = 0.000) for 1328 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2610 (Rfree = 0.000) for 1318 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.92 3.72 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 87 peptides, 14 chains. Longest chain 14 peptides. Score 0.408 Round 2: 92 peptides, 14 chains. Longest chain 12 peptides. Score 0.442 Round 3: 106 peptides, 16 chains. Longest chain 16 peptides. Score 0.475 Round 4: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.401 Round 5: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.430 Taking the results from Round 3 Chains 16, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 2968 restraints for refining 1361 atoms. 2624 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2922 (Rfree = 0.000) for 1361 atoms. Found 6 (6 requested) and removed 23 (3 requested) atoms. Cycle 17: After refmac, R = 0.2615 (Rfree = 0.000) for 1332 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2786 (Rfree = 0.000) for 1320 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2514 (Rfree = 0.000) for 1307 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 20: After refmac, R = 0.2554 (Rfree = 0.000) for 1297 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.88 3.68 Search for helices and strands: 0 residues in 0 chains, 1362 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 6 peptides. Score 0.248 Round 2: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.392 Round 3: 107 peptides, 16 chains. Longest chain 14 peptides. Score 0.481 Round 4: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.421 Round 5: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.489 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 3072 restraints for refining 1359 atoms. 2731 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2953 (Rfree = 0.000) for 1359 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 22: After refmac, R = 0.2790 (Rfree = 0.000) for 1327 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 23: After refmac, R = 0.2780 (Rfree = 0.000) for 1313 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 24: After refmac, R = 0.2727 (Rfree = 0.000) for 1305 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.2673 (Rfree = 0.000) for 1300 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.98 3.77 Search for helices and strands: 0 residues in 0 chains, 1360 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.240 Round 2: 90 peptides, 16 chains. Longest chain 8 peptides. Score 0.369 Round 3: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.383 Round 4: 92 peptides, 15 chains. Longest chain 9 peptides. Score 0.413 Round 5: 100 peptides, 15 chains. Longest chain 10 peptides. Score 0.465 Taking the results from Round 5 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 2877 restraints for refining 1295 atoms. 2552 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2928 (Rfree = 0.000) for 1295 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2863 (Rfree = 0.000) for 1277 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2824 (Rfree = 0.000) for 1263 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 29: After refmac, R = 0.2569 (Rfree = 0.000) for 1252 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 30: After refmac, R = 0.2919 (Rfree = 0.000) for 1248 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.95 3.74 Search for helices and strands: 0 residues in 0 chains, 1312 seeds are put forward Round 1: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.320 Round 2: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.383 Round 3: 87 peptides, 15 chains. Longest chain 13 peptides. Score 0.378 Round 4: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.408 Round 5: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 4 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 3112 restraints for refining 1339 atoms. 2834 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3023 (Rfree = 0.000) for 1339 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.2843 (Rfree = 0.000) for 1318 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.3088 (Rfree = 0.000) for 1302 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 34: After refmac, R = 0.3089 (Rfree = 0.000) for 1286 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 35: After refmac, R = 0.2859 (Rfree = 0.000) for 1270 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.67 Search for helices and strands: 0 residues in 0 chains, 1361 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.244 Round 2: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.322 Round 3: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.373 Round 4: 72 peptides, 11 chains. Longest chain 13 peptides. Score 0.397 Round 5: 72 peptides, 11 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 2979 restraints for refining 1332 atoms. 2746 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3027 (Rfree = 0.000) for 1332 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 37: After refmac, R = 0.2913 (Rfree = 0.000) for 1302 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 38: After refmac, R = 0.2952 (Rfree = 0.000) for 1278 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 39: After refmac, R = 0.2809 (Rfree = 0.000) for 1268 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.2885 (Rfree = 0.000) for 1259 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.90 3.70 Search for helices and strands: 0 residues in 0 chains, 1318 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 2: 65 peptides, 13 chains. Longest chain 10 peptides. Score 0.278 Round 3: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.315 Round 4: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.357 Round 5: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2308 reflections ( 99.78 % complete ) and 3086 restraints for refining 1360 atoms. 2842 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2825 (Rfree = 0.000) for 1360 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 42: After refmac, R = 0.2731 (Rfree = 0.000) for 1333 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.2645 (Rfree = 0.000) for 1324 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 44: After refmac, R = 0.2774 (Rfree = 0.000) for 1315 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 45: After refmac, R = 0.2412 (Rfree = 0.000) for 1306 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 1365 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.225 Round 2: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.288 Round 3: 69 peptides, 13 chains. Longest chain 7 peptides. Score 0.309 Round 4: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.330 Round 5: 85 peptides, 14 chains. Longest chain 14 peptides. Score 0.395 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 71, 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 1vk2-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2308 reflections ( 99.78 % complete ) and 2821 restraints for refining 1295 atoms. 2551 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2709 (Rfree = 0.000) for 1295 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2729 (Rfree = 0.000) for 1282 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2666 (Rfree = 0.000) for 1273 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2526 (Rfree = 0.000) for 1266 atoms. TimeTaking 28.78