null Sun 23 Dec 22:22:52 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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/1vkb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 22:23:02 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkb-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 131 and 0 Target number of residues in the AU: 131 Target solvent content: 0.6103 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-3.8-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: 170 Cell parameters: 85.745 85.745 42.858 90.000 90.000 120.000 Input sequence file: 1vkb-3.8-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 3.803 Wilson plot Bfac: 56.28 1849 reflections ( 99.89 % complete ) and 0 restraints for refining 1437 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3789 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3765 (Rfree = 0.000) for 1437 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.226 Round 2: 54 peptides, 10 chains. Longest chain 11 peptides. Score 0.319 Round 3: 61 peptides, 11 chains. Longest chain 12 peptides. Score 0.345 Round 4: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.431 Round 5: 65 peptides, 11 chains. Longest chain 11 peptides. Score 0.383 Taking the results from Round 4 Chains 8, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2915 restraints for refining 1165 atoms. 2727 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3616 (Rfree = 0.000) for 1165 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 2: After refmac, R = 0.3225 (Rfree = 0.000) for 1137 atoms. Found 3 (6 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.2847 (Rfree = 0.000) for 1120 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2674 (Rfree = 0.000) for 1108 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 5: After refmac, R = 0.2509 (Rfree = 0.000) for 1101 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1107 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.276 Round 2: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.282 Round 3: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.302 Round 4: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.359 Round 5: 72 peptides, 12 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 5 Chains 12, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2570 restraints for refining 1092 atoms. 2342 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2886 (Rfree = 0.000) for 1092 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 7: After refmac, R = 0.2733 (Rfree = 0.000) for 1082 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 8: After refmac, R = 0.2125 (Rfree = 0.000) for 1071 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2233 (Rfree = 0.000) for 1069 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 10: After refmac, R = 0.2075 (Rfree = 0.000) for 1059 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1083 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.328 Round 2: 70 peptides, 11 chains. Longest chain 16 peptides. Score 0.427 Round 3: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.395 Round 4: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.445 Round 5: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.349 Taking the results from Round 4 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2700 restraints for refining 1152 atoms. 2467 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3047 (Rfree = 0.000) for 1152 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2617 (Rfree = 0.000) for 1142 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2687 (Rfree = 0.000) for 1136 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2361 (Rfree = 0.000) for 1129 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2317 (Rfree = 0.000) for 1126 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1146 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.262 Round 2: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.340 Round 3: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.365 Round 4: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.445 Round 5: 80 peptides, 13 chains. Longest chain 9 peptides. Score 0.438 Taking the results from Round 4 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2648 restraints for refining 1164 atoms. 2387 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2897 (Rfree = 0.000) for 1164 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2653 (Rfree = 0.000) for 1142 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2388 (Rfree = 0.000) for 1139 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2642 (Rfree = 0.000) for 1135 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 20: After refmac, R = 0.2296 (Rfree = 0.000) for 1131 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 1161 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.323 Round 2: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.414 Round 3: 82 peptides, 12 chains. Longest chain 18 peptides. Score 0.490 Round 4: 66 peptides, 12 chains. Longest chain 12 peptides. Score 0.352 Round 5: 84 peptides, 13 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 3 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2725 restraints for refining 1165 atoms. 2457 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2668 (Rfree = 0.000) for 1165 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2627 (Rfree = 0.000) for 1153 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2291 (Rfree = 0.000) for 1146 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2300 (Rfree = 0.000) for 1137 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.2348 (Rfree = 0.000) for 1128 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1155 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 10 peptides. Score 0.257 Round 2: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.377 Round 3: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.340 Round 4: 80 peptides, 13 chains. Longest chain 15 peptides. Score 0.438 Round 5: 87 peptides, 13 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 5 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2609 restraints for refining 1159 atoms. 2310 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2505 (Rfree = 0.000) for 1159 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.2457 (Rfree = 0.000) for 1150 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2287 (Rfree = 0.000) for 1148 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 29: After refmac, R = 0.2278 (Rfree = 0.000) for 1140 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2323 (Rfree = 0.000) for 1137 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 1155 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.299 Round 2: 64 peptides, 11 chains. Longest chain 15 peptides. Score 0.374 Round 3: 66 peptides, 10 chains. Longest chain 13 peptides. Score 0.431 Round 4: 63 peptides, 10 chains. Longest chain 13 peptides. Score 0.405 Round 5: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 3 Chains 10, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2700 restraints for refining 1136 atoms. 2486 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2466 (Rfree = 0.000) for 1136 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 32: After refmac, R = 0.2176 (Rfree = 0.000) for 1127 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. Cycle 33: After refmac, R = 0.2169 (Rfree = 0.000) for 1116 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2035 (Rfree = 0.000) for 1112 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2056 (Rfree = 0.000) for 1105 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 1127 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.250 Round 2: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.355 Round 3: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.345 Round 4: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.414 Round 5: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.415 Taking the results from Round 5 Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2644 restraints for refining 1139 atoms. 2412 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2498 (Rfree = 0.000) for 1139 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 37: After refmac, R = 0.2403 (Rfree = 0.000) for 1131 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2201 (Rfree = 0.000) for 1128 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.2124 (Rfree = 0.000) for 1125 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1981 (Rfree = 0.000) for 1124 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 1137 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.309 Round 2: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.349 Round 3: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.355 Round 4: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.355 Round 5: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 5 Chains 10, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1849 reflections ( 99.89 % complete ) and 2781 restraints for refining 1164 atoms. 2587 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2309 (Rfree = 0.000) for 1164 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.2486 (Rfree = 0.000) for 1162 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.2026 (Rfree = 0.000) for 1161 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.1994 (Rfree = 0.000) for 1154 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2037 (Rfree = 0.000) for 1152 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1166 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.213 Round 2: 61 peptides, 12 chains. Longest chain 12 peptides. Score 0.304 Round 3: 50 peptides, 9 chains. Longest chain 8 peptides. Score 0.323 Round 4: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.260 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 38, 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. 1849 reflections ( 99.89 % complete ) and 2884 restraints for refining 1165 atoms. 2740 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2078 (Rfree = 0.000) for 1165 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1936 (Rfree = 0.000) for 1161 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2085 (Rfree = 0.000) for 1156 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2021 (Rfree = 0.000) for 1151 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:18 GMT 2018 Job finished. TimeTaking 26.42 Used memory is bytes: 13617584