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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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/1vkb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 22:23:12 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 128 and 0 Target number of residues in the AU: 128 Target solvent content: 0.6192 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-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: 170 Cell parameters: 85.745 85.745 42.858 90.000 90.000 120.000 Input sequence file: 1vkb-4.0-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 4.008 Wilson plot Bfac: 60.20 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1589 reflections ( 99.87 % complete ) and 0 restraints for refining 1427 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3926 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4159 (Rfree = 0.000) for 1427 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.180 Round 2: 41 peptides, 9 chains. Longest chain 8 peptides. Score 0.226 Round 3: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.327 Round 4: 58 peptides, 9 chains. Longest chain 13 peptides. Score 0.400 Round 5: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.405 Taking the results from Round 5 Chains 10, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2655 restraints for refining 1107 atoms. 2453 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3981 (Rfree = 0.000) for 1107 atoms. Found 5 (5 requested) and removed 29 (2 requested) atoms. Cycle 2: After refmac, R = 0.3429 (Rfree = 0.000) for 1067 atoms. Found 5 (5 requested) and removed 31 (2 requested) atoms. Cycle 3: After refmac, R = 0.3071 (Rfree = 0.000) for 1031 atoms. Found 3 (4 requested) and removed 33 (2 requested) atoms. Cycle 4: After refmac, R = 0.2698 (Rfree = 0.000) for 993 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 5: After refmac, R = 0.2672 (Rfree = 0.000) for 977 atoms. Found 2 (4 requested) and removed 11 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 984 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.221 Round 2: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.252 Round 3: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.262 Round 4: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.361 Round 5: 65 peptides, 13 chains. Longest chain 6 peptides. Score 0.302 Taking the results from Round 4 Chains 12, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2451 restraints for refining 1031 atoms. 2243 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2786 (Rfree = 0.000) for 1031 atoms. Found 3 (4 requested) and removed 9 (2 requested) atoms. Cycle 7: After refmac, R = 0.3011 (Rfree = 0.000) for 1020 atoms. Found 4 (4 requested) and removed 15 (2 requested) atoms. Cycle 8: After refmac, R = 0.2753 (Rfree = 0.000) for 1006 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2623 (Rfree = 0.000) for 1000 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2541 (Rfree = 0.000) for 994 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 1005 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 5 peptides. Score 0.231 Round 2: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.338 Round 3: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.374 Round 4: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.386 Round 5: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.410 Taking the results from Round 5 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2521 restraints for refining 1092 atoms. 2267 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3253 (Rfree = 0.000) for 1092 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2906 (Rfree = 0.000) for 1077 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 13: After refmac, R = 0.2800 (Rfree = 0.000) for 1063 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.2714 (Rfree = 0.000) for 1060 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2660 (Rfree = 0.000) for 1058 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 1086 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 13 peptides. Score 0.309 Round 2: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.356 Round 3: 83 peptides, 14 chains. Longest chain 12 peptides. Score 0.427 Round 4: 82 peptides, 13 chains. Longest chain 13 peptides. Score 0.455 Round 5: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.395 Taking the results from Round 4 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2667 restraints for refining 1135 atoms. 2404 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2992 (Rfree = 0.000) for 1135 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 17: After refmac, R = 0.2672 (Rfree = 0.000) for 1119 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2719 (Rfree = 0.000) for 1115 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 19: After refmac, R = 0.2471 (Rfree = 0.000) for 1110 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2604 (Rfree = 0.000) for 1108 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1140 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 9 peptides. Score 0.245 Round 2: 74 peptides, 14 chains. Longest chain 15 peptides. Score 0.347 Round 3: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.383 Round 4: 72 peptides, 12 chains. Longest chain 14 peptides. Score 0.407 Round 5: 70 peptides, 13 chains. Longest chain 13 peptides. Score 0.349 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 ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2821 restraints for refining 1161 atoms. 2593 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3349 (Rfree = 0.000) for 1161 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 22: After refmac, R = 0.2659 (Rfree = 0.000) for 1148 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.2306 (Rfree = 0.000) for 1148 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 24: After refmac, R = 0.2102 (Rfree = 0.000) for 1145 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2104 (Rfree = 0.000) for 1145 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 1164 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.202 Round 2: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.299 Round 3: 55 peptides, 10 chains. Longest chain 11 peptides. Score 0.329 Round 4: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.309 Round 5: 61 peptides, 10 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 5 Chains 10, Residues 51, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2711 restraints for refining 1158 atoms. 2496 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2372 (Rfree = 0.000) for 1158 atoms. Found 3 (5 requested) and removed 9 (2 requested) atoms. Cycle 27: After refmac, R = 0.2135 (Rfree = 0.000) for 1146 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.2452 (Rfree = 0.000) for 1144 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.2022 (Rfree = 0.000) for 1144 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.1933 (Rfree = 0.000) for 1141 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 1159 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.272 Round 2: 60 peptides, 12 chains. Longest chain 10 peptides. Score 0.294 Round 3: 70 peptides, 11 chains. Longest chain 13 peptides. Score 0.427 Round 4: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.440 Round 5: 60 peptides, 12 chains. Longest chain 6 peptides. Score 0.294 Taking the results from Round 4 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2750 restraints for refining 1163 atoms. 2516 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2328 (Rfree = 0.000) for 1163 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.2275 (Rfree = 0.000) for 1162 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 33: After refmac, R = 0.2483 (Rfree = 0.000) for 1158 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 34: After refmac, R = 0.1817 (Rfree = 0.000) for 1156 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 35: After refmac, R = 0.2095 (Rfree = 0.000) for 1153 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1163 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.255 Round 2: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.329 Round 3: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.286 Round 4: 67 peptides, 12 chains. Longest chain 10 peptides. Score 0.361 Round 5: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.340 Taking the results from Round 4 Chains 12, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2804 restraints for refining 1163 atoms. 2596 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2719 (Rfree = 0.000) for 1163 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.2144 (Rfree = 0.000) for 1154 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.1899 (Rfree = 0.000) for 1151 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 39: After refmac, R = 0.1891 (Rfree = 0.000) for 1147 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.1988 (Rfree = 0.000) for 1143 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1168 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.230 Round 2: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.321 Round 3: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.377 Round 4: 71 peptides, 10 chains. Longest chain 11 peptides. Score 0.474 Round 5: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 4 Chains 10, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1589 reflections ( 99.87 % complete ) and 2715 restraints for refining 1163 atoms. 2481 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3186 (Rfree = 0.000) for 1163 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 42: After refmac, R = 0.2486 (Rfree = 0.000) for 1159 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 43: After refmac, R = 0.2675 (Rfree = 0.000) for 1155 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 44: After refmac, R = 0.2596 (Rfree = 0.000) for 1147 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2649 (Rfree = 0.000) for 1147 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 1167 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 7 peptides. Score 0.222 Round 2: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.294 Round 3: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.292 Round 4: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.352 Round 5: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.316 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 54, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1589 reflections ( 99.87 % complete ) and 2802 restraints for refining 1163 atoms. 2598 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2296 (Rfree = 0.000) for 1163 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2117 (Rfree = 0.000) for 1158 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2097 (Rfree = 0.000) for 1155 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1900 (Rfree = 0.000) for 1152 atoms. TimeTaking 25.85