Sun 23 Dec 22:23:02 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-3.6-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 22:23:12 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-3.6-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.5984 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1288 target number of atoms Had to go as low as 0.75 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 3.605 Wilson plot Bfac: 51.89 2163 reflections ( 99.91 % complete ) and 0 restraints for refining 1429 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3763 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3498 (Rfree = 0.000) for 1429 atoms. Found 9 (9 requested) and removed 30 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 6 peptides. Score 0.202 Round 2: 74 peptides, 16 chains. Longest chain 9 peptides. Score 0.268 Round 3: 79 peptides, 17 chains. Longest chain 6 peptides. Score 0.276 Round 4: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.361 Round 5: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 5 Chains 13, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2742 restraints for refining 1168 atoms. 2519 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2769 (Rfree = 0.000) for 1168 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2773 (Rfree = 0.000) for 1150 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2404 (Rfree = 0.000) for 1144 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2741 (Rfree = 0.000) for 1133 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2277 (Rfree = 0.000) for 1130 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 1151 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.328 Round 2: 74 peptides, 14 chains. Longest chain 12 peptides. Score 0.347 Round 3: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.365 Round 4: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.395 Round 5: 71 peptides, 11 chains. Longest chain 9 peptides. Score 0.436 Taking the results from Round 5 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2689 restraints for refining 1168 atoms. 2404 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2680 (Rfree = 0.000) for 1168 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2422 (Rfree = 0.000) for 1157 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2275 (Rfree = 0.000) for 1150 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2222 (Rfree = 0.000) for 1147 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 10: After refmac, R = 0.2159 (Rfree = 0.000) for 1142 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1170 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.304 Round 2: 73 peptides, 13 chains. Longest chain 7 peptides. Score 0.377 Round 3: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.333 Round 4: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.340 Round 5: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 2 Chains 13, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2672 restraints for refining 1132 atoms. 2445 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2532 (Rfree = 0.000) for 1132 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2469 (Rfree = 0.000) for 1121 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2136 (Rfree = 0.000) for 1118 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2319 (Rfree = 0.000) for 1114 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2110 (Rfree = 0.000) for 1116 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1140 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.252 Round 2: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.356 Round 3: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.334 Round 4: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.399 Round 5: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.430 Taking the results from Round 5 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2705 restraints for refining 1167 atoms. 2454 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2424 (Rfree = 0.000) for 1167 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 17: After refmac, R = 0.2499 (Rfree = 0.000) for 1161 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2265 (Rfree = 0.000) for 1160 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2394 (Rfree = 0.000) for 1159 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2218 (Rfree = 0.000) for 1158 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 1178 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 10 peptides. Score 0.290 Round 2: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.345 Round 3: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.392 Round 4: 75 peptides, 10 chains. Longest chain 11 peptides. Score 0.506 Round 5: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.390 Taking the results from Round 4 Chains 10, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2687 restraints for refining 1168 atoms. 2437 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2719 (Rfree = 0.000) for 1168 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 22: After refmac, R = 0.2506 (Rfree = 0.000) for 1168 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2456 (Rfree = 0.000) for 1169 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2070 (Rfree = 0.000) for 1165 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2044 (Rfree = 0.000) for 1166 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.10 Search for helices and strands: 0 residues in 0 chains, 1186 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 9 peptides. Score 0.240 Round 2: 63 peptides, 13 chains. Longest chain 9 peptides. Score 0.282 Round 3: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.368 Round 4: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.407 Round 5: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.302 Taking the results from Round 4 Chains 12, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2812 restraints for refining 1168 atoms. 2584 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2310 (Rfree = 0.000) for 1168 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2187 (Rfree = 0.000) for 1164 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2009 (Rfree = 0.000) for 1161 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2176 (Rfree = 0.000) for 1164 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.1826 (Rfree = 0.000) for 1163 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 1176 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.252 Round 2: 76 peptides, 16 chains. Longest chain 9 peptides. Score 0.287 Round 3: 78 peptides, 17 chains. Longest chain 9 peptides. Score 0.267 Round 4: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.383 Round 5: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.258 Taking the results from Round 4 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2718 restraints for refining 1167 atoms. 2476 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2258 (Rfree = 0.000) for 1167 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.2125 (Rfree = 0.000) for 1163 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.2054 (Rfree = 0.000) for 1160 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2338 (Rfree = 0.000) for 1157 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2092 (Rfree = 0.000) for 1158 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 1194 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.300 Round 2: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.392 Round 3: 70 peptides, 13 chains. Longest chain 7 peptides. Score 0.349 Round 4: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.398 Round 5: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.435 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2567 restraints for refining 1168 atoms. 2277 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2520 (Rfree = 0.000) for 1168 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2205 (Rfree = 0.000) for 1161 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2188 (Rfree = 0.000) for 1160 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.1967 (Rfree = 0.000) for 1161 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1931 (Rfree = 0.000) for 1161 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 1182 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.242 Round 2: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.306 Round 3: 56 peptides, 8 chains. Longest chain 12 peptides. Score 0.423 Round 4: 53 peptides, 10 chains. Longest chain 10 peptides. Score 0.309 Round 5: 54 peptides, 9 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 3 Chains 8, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2163 reflections ( 99.91 % complete ) and 2676 restraints for refining 1168 atoms. 2492 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2002 (Rfree = 0.000) for 1168 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.1912 (Rfree = 0.000) for 1165 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.1878 (Rfree = 0.000) for 1163 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.1732 (Rfree = 0.000) for 1162 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1706 (Rfree = 0.000) for 1160 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1184 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 10 peptides. Score 0.274 Round 2: 66 peptides, 13 chains. Longest chain 12 peptides. Score 0.311 Round 3: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.352 Round 4: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.333 Round 5: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 58, 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. 2163 reflections ( 99.91 % complete ) and 2645 restraints for refining 1168 atoms. 2424 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1940 (Rfree = 0.000) for 1168 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2010 (Rfree = 0.000) for 1160 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1917 (Rfree = 0.000) for 1157 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1822 (Rfree = 0.000) for 1153 atoms. TimeTaking 26.55