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 1vkb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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/1vkb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 22:23:15 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/1vkb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 138 and 0 Target number of residues in the AU: 138 Target solvent content: 0.5895 Checking the provided sequence file Detected sequence length: 161 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 161 Adjusted target solvent content: 0.52 Input MTZ file: 1vkb-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: 170 Cell parameters: 85.745 85.745 42.858 90.000 90.000 120.000 Input sequence file: 1vkb-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1288 target number of atoms Had to go as low as 0.70 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: 74.257 3.406 Wilson plot Bfac: 48.21 2571 reflections ( 99.92 % complete ) and 0 restraints for refining 1432 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3701 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3884 (Rfree = 0.000) for 1432 atoms. Found 10 (10 requested) and removed 32 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1424 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.234 Round 2: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.260 Round 3: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.309 Round 4: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.343 Round 5: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.340 Taking the results from Round 4 Chains 12, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2676 restraints for refining 1170 atoms. 2476 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2997 (Rfree = 0.000) for 1170 atoms. Found 1 (8 requested) and removed 9 (4 requested) atoms. Cycle 2: After refmac, R = 0.2785 (Rfree = 0.000) for 1152 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2783 (Rfree = 0.000) for 1145 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2777 (Rfree = 0.000) for 1140 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2761 (Rfree = 0.000) for 1135 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 2.98 Search for helices and strands: 0 residues in 0 chains, 1164 seeds are put forward Round 1: 59 peptides, 14 chains. Longest chain 5 peptides. Score 0.199 Round 2: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.328 Round 3: 66 peptides, 10 chains. Longest chain 13 peptides. Score 0.431 Round 4: 77 peptides, 14 chains. Longest chain 13 peptides. Score 0.374 Round 5: 70 peptides, 11 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 3 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2712 restraints for refining 1171 atoms. 2470 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2716 (Rfree = 0.000) for 1171 atoms. Found 4 (8 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2514 (Rfree = 0.000) for 1156 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2816 (Rfree = 0.000) for 1148 atoms. Found 6 (8 requested) and removed 15 (4 requested) atoms. Cycle 9: After refmac, R = 0.2383 (Rfree = 0.000) for 1137 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2490 (Rfree = 0.000) for 1129 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 2.95 Search for helices and strands: 0 residues in 0 chains, 1159 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.279 Round 2: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.421 Round 3: 88 peptides, 12 chains. Longest chain 17 peptides. Score 0.536 Round 4: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.374 Round 5: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.435 Taking the results from Round 3 Chains 12, Residues 76, Estimated correctness of the model 5.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2692 restraints for refining 1171 atoms. 2400 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2452 (Rfree = 0.000) for 1171 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 12: After refmac, R = 0.2376 (Rfree = 0.000) for 1168 atoms. Found 4 (8 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2338 (Rfree = 0.000) for 1159 atoms. Found 3 (8 requested) and removed 14 (4 requested) atoms. Cycle 14: After refmac, R = 0.2311 (Rfree = 0.000) for 1148 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.2230 (Rfree = 0.000) for 1140 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.02 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.343 Round 2: 76 peptides, 12 chains. Longest chain 12 peptides. Score 0.441 Round 3: 81 peptides, 13 chains. Longest chain 12 peptides. Score 0.447 Round 4: 67 peptides, 11 chains. Longest chain 12 peptides. Score 0.401 Round 5: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 3 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2587 restraints for refining 1171 atoms. 2296 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2448 (Rfree = 0.000) for 1171 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2257 (Rfree = 0.000) for 1167 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.2179 (Rfree = 0.000) for 1161 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2071 (Rfree = 0.000) for 1158 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2036 (Rfree = 0.000) for 1154 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 1175 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 9 peptides. Score 0.282 Round 2: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.438 Round 3: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.383 Round 4: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.415 Round 5: 79 peptides, 13 chains. Longest chain 10 peptides. Score 0.430 Taking the results from Round 2 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2661 restraints for refining 1171 atoms. 2406 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2465 (Rfree = 0.000) for 1171 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2364 (Rfree = 0.000) for 1175 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2269 (Rfree = 0.000) for 1174 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2238 (Rfree = 0.000) for 1171 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2214 (Rfree = 0.000) for 1167 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 2.97 Search for helices and strands: 0 residues in 0 chains, 1194 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.323 Round 2: 70 peptides, 11 chains. Longest chain 13 peptides. Score 0.427 Round 3: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.407 Round 4: 83 peptides, 13 chains. Longest chain 10 peptides. Score 0.463 Round 5: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.372 Taking the results from Round 4 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2595 restraints for refining 1171 atoms. 2307 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2501 (Rfree = 0.000) for 1171 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2260 (Rfree = 0.000) for 1167 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2152 (Rfree = 0.000) for 1169 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2145 (Rfree = 0.000) for 1164 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 1164 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 1179 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.282 Round 2: 69 peptides, 15 chains. Longest chain 6 peptides. Score 0.259 Round 3: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.363 Round 4: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.450 Round 5: 74 peptides, 10 chains. Longest chain 13 peptides. Score 0.498 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2634 restraints for refining 1171 atoms. 2356 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2759 (Rfree = 0.000) for 1171 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.2268 (Rfree = 0.000) for 1171 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2187 (Rfree = 0.000) for 1170 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2243 (Rfree = 0.000) for 1163 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2236 (Rfree = 0.000) for 1159 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.06 Search for helices and strands: 0 residues in 0 chains, 1181 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.259 Round 2: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.364 Round 3: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.345 Round 4: 66 peptides, 13 chains. Longest chain 10 peptides. Score 0.311 Round 5: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.306 Taking the results from Round 2 Chains 11, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2877 restraints for refining 1171 atoms. 2680 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2363 (Rfree = 0.000) for 1171 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2428 (Rfree = 0.000) for 1169 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2506 (Rfree = 0.000) for 1168 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2436 (Rfree = 0.000) for 1172 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2304 (Rfree = 0.000) for 1167 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.09 Search for helices and strands: 0 residues in 0 chains, 1177 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.296 Round 2: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.314 Round 3: 62 peptides, 10 chains. Longest chain 9 peptides. Score 0.396 Round 4: 64 peptides, 10 chains. Longest chain 9 peptides. Score 0.414 Round 5: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 4 Chains 10, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2571 reflections ( 99.92 % complete ) and 2717 restraints for refining 1171 atoms. 2511 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2632 (Rfree = 0.000) for 1171 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2458 (Rfree = 0.000) for 1170 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2404 (Rfree = 0.000) for 1174 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2406 (Rfree = 0.000) for 1170 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2392 (Rfree = 0.000) for 1170 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1187 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.289 Round 2: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.371 Round 3: 76 peptides, 12 chains. Longest chain 9 peptides. Score 0.441 Round 4: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.374 Round 5: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.314 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 64, 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 1vkb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2571 reflections ( 99.92 % complete ) and 2674 restraints for refining 1171 atoms. 2430 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2560 (Rfree = 0.000) for 1171 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2533 (Rfree = 0.000) for 1166 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2632 (Rfree = 0.000) for 1161 atoms. Found 0 (8 requested) and removed 0 (4 requested) atoms. Cycle 49: After refmac, R = 0.2370 (Rfree = 0.000) for 1161 atoms. TimeTaking 26.7