Mon 24 Dec 00:13:00 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2obp-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.8-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:13:04 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.8-parrot-mrncs/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: 0.6745 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-3.8-parrot-mrncs.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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.462 3.801 Wilson plot Bfac: 94.70 2661 reflections ( 99.18 % complete ) and 0 restraints for refining 1706 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3657 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4007 (Rfree = 0.000) for 1706 atoms. Found 9 (9 requested) and removed 27 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.54 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 0 residues added, 1721 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.287 Round 2: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.378 Round 3: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.424 Round 4: 85 peptides, 10 chains. Longest chain 17 peptides. Score 0.515 Round 5: 89 peptides, 12 chains. Longest chain 12 peptides. Score 0.483 Taking the results from Round 4 Chains 10, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 3206 restraints for refining 1312 atoms. 2916 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3532 (Rfree = 0.000) for 1312 atoms. Found 7 (7 requested) and removed 22 (3 requested) atoms. Cycle 2: After refmac, R = 0.3427 (Rfree = 0.000) for 1270 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.3361 (Rfree = 0.000) for 1234 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 4: After refmac, R = 0.3209 (Rfree = 0.000) for 1212 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 5: After refmac, R = 0.3177 (Rfree = 0.000) for 1196 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.53 Search for helices and strands: 0 residues in 0 chains, 1260 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 1287 seeds are put forward Round 1: 86 peptides, 15 chains. Longest chain 13 peptides. Score 0.373 Round 2: 83 peptides, 12 chains. Longest chain 12 peptides. Score 0.444 Round 3: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.467 Round 4: 88 peptides, 14 chains. Longest chain 10 peptides. Score 0.418 Round 5: 87 peptides, 13 chains. Longest chain 11 peptides. Score 0.441 Taking the results from Round 3 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2580 restraints for refining 1205 atoms. 2265 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3148 (Rfree = 0.000) for 1205 atoms. Found 5 (6 requested) and removed 13 (3 requested) atoms. Cycle 7: After refmac, R = 0.3106 (Rfree = 0.000) for 1173 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.3147 (Rfree = 0.000) for 1151 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 9: After refmac, R = 0.2957 (Rfree = 0.000) for 1130 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 10: After refmac, R = 0.2944 (Rfree = 0.000) for 1119 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.57 Search for helices and strands: 0 residues in 0 chains, 1195 seeds are put forward NCS extension: 0 residues added, 1195 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.324 Round 2: 86 peptides, 12 chains. Longest chain 12 peptides. Score 0.464 Round 3: 86 peptides, 12 chains. Longest chain 13 peptides. Score 0.464 Round 4: 86 peptides, 12 chains. Longest chain 12 peptides. Score 0.464 Round 5: 91 peptides, 11 chains. Longest chain 17 peptides. Score 0.524 Taking the results from Round 5 Chains 11, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2782 restraints for refining 1243 atoms. 2473 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3555 (Rfree = 0.000) for 1243 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 12: After refmac, R = 0.3256 (Rfree = 0.000) for 1210 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.2996 (Rfree = 0.000) for 1181 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.3110 (Rfree = 0.000) for 1156 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 15: After refmac, R = 0.3161 (Rfree = 0.000) for 1130 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 1209 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1223 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.326 Round 2: 80 peptides, 10 chains. Longest chain 18 peptides. Score 0.484 Round 3: 85 peptides, 11 chains. Longest chain 14 peptides. Score 0.487 Round 4: 90 peptides, 11 chains. Longest chain 12 peptides. Score 0.518 Round 5: 92 peptides, 10 chains. Longest chain 17 peptides. Score 0.557 Taking the results from Round 5 Chains 10, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2563 restraints for refining 1180 atoms. 2245 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3499 (Rfree = 0.000) for 1180 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 17: After refmac, R = 0.3419 (Rfree = 0.000) for 1147 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 18: After refmac, R = 0.3398 (Rfree = 0.000) for 1132 atoms. Found 6 (6 requested) and removed 128 (3 requested) atoms. Cycle 19: After refmac, R = 0.3589 (Rfree = 0.000) for 999 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 20: After refmac, R = 0.3552 (Rfree = 0.000) for 973 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.50 Search for helices and strands: 0 residues in 0 chains, 1023 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 1033 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 7 peptides. Score 0.319 Round 2: 79 peptides, 12 chains. Longest chain 12 peptides. Score 0.417 Round 3: 91 peptides, 15 chains. Longest chain 14 peptides. Score 0.408 Round 4: 94 peptides, 12 chains. Longest chain 14 peptides. Score 0.514 Round 5: 88 peptides, 12 chains. Longest chain 11 peptides. Score 0.477 Taking the results from Round 4 Chains 13, Residues 82, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2290 restraints for refining 1108 atoms. 1948 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3614 (Rfree = 0.000) for 1108 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 22: After refmac, R = 0.3511 (Rfree = 0.000) for 1086 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. Cycle 23: After refmac, R = 0.3254 (Rfree = 0.000) for 1059 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.3523 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 25: After refmac, R = 0.3103 (Rfree = 0.000) for 1043 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.53 Search for helices and strands: 0 residues in 0 chains, 1137 seeds are put forward NCS extension: 0 residues added, 1137 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.344 Round 2: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.381 Round 3: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.417 Round 4: 85 peptides, 12 chains. Longest chain 17 peptides. Score 0.457 Round 5: 75 peptides, 10 chains. Longest chain 12 peptides. Score 0.451 Taking the results from Round 4 Chains 12, Residues 73, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2478 restraints for refining 1159 atoms. 2182 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3477 (Rfree = 0.000) for 1159 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 27: After refmac, R = 0.3283 (Rfree = 0.000) for 1127 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.3369 (Rfree = 0.000) for 1107 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 29: After refmac, R = 0.3275 (Rfree = 0.000) for 1091 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.3511 (Rfree = 0.000) for 1076 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.97 3.66 Search for helices and strands: 0 residues in 0 chains, 1145 seeds are put forward NCS extension: 0 residues added, 1145 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.263 Round 2: 79 peptides, 14 chains. Longest chain 8 peptides. Score 0.354 Round 3: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.355 Round 4: 77 peptides, 13 chains. Longest chain 8 peptides. Score 0.371 Round 5: 81 peptides, 13 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 5 Chains 13, Residues 68, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2391 restraints for refining 1152 atoms. 2118 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3582 (Rfree = 0.000) for 1152 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.3227 (Rfree = 0.000) for 1131 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.2893 (Rfree = 0.000) for 1113 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.3099 (Rfree = 0.000) for 1099 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.3173 (Rfree = 0.000) for 1097 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 3.55 Search for helices and strands: 0 residues in 0 chains, 1156 seeds are put forward NCS extension: 0 residues added, 1156 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 12 peptides. Score 0.332 Round 2: 82 peptides, 13 chains. Longest chain 13 peptides. Score 0.407 Round 3: 73 peptides, 13 chains. Longest chain 9 peptides. Score 0.341 Round 4: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.364 Round 5: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 2 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2315 restraints for refining 1100 atoms. 2052 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3346 (Rfree = 0.000) for 1100 atoms. Found 6 (6 requested) and removed 135 (3 requested) atoms. Cycle 37: After refmac, R = 0.3569 (Rfree = 0.000) for 954 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.3386 (Rfree = 0.000) for 945 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.3206 (Rfree = 0.000) for 939 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.3160 (Rfree = 0.000) for 937 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.50 Search for helices and strands: 0 residues in 0 chains, 1013 seeds are put forward NCS extension: 0 residues added, 1013 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.246 Round 2: 71 peptides, 13 chains. Longest chain 11 peptides. Score 0.326 Round 3: 72 peptides, 13 chains. Longest chain 13 peptides. Score 0.334 Round 4: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.326 Round 5: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 5 Chains 13, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2429 restraints for refining 1106 atoms. 2194 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3641 (Rfree = 0.000) for 1106 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 42: After refmac, R = 0.3486 (Rfree = 0.000) for 1090 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.3535 (Rfree = 0.000) for 1075 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 44: After refmac, R = 0.3427 (Rfree = 0.000) for 1067 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.3461 (Rfree = 0.000) for 1056 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.52 Search for helices and strands: 0 residues in 0 chains, 1118 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1121 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.239 Round 2: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.314 Round 3: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.277 Round 4: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.275 Round 5: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.268 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 63, 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 2obp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2661 reflections ( 99.18 % complete ) and 2321 restraints for refining 1061 atoms. 2084 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3684 (Rfree = 0.000) for 1061 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3505 (Rfree = 0.000) for 1054 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.3594 (Rfree = 0.000) for 1044 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.3430 (Rfree = 0.000) for 1037 atoms. TimeTaking 28.58