Sun 23 Dec 22:22:43 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 2obp-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obp-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obp-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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/2obp-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 22:22:52 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/2obp-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 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-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 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 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 1704 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3674 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3898 (Rfree = 0.000) for 1704 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.91 3.61 Search for helices and strands: 0 residues in 0 chains, 1730 seeds are put forward NCS extension: 0 residues added, 1730 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.231 Round 2: 75 peptides, 11 chains. Longest chain 11 peptides. Score 0.420 Round 3: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.427 Round 4: 98 peptides, 13 chains. Longest chain 21 peptides. Score 0.511 Round 5: 98 peptides, 12 chains. Longest chain 14 peptides. Score 0.538 Taking the results from Round 5 Chains 12, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2917 restraints for refining 1267 atoms. 2585 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3379 (Rfree = 0.000) for 1267 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 2: After refmac, R = 0.3413 (Rfree = 0.000) for 1219 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 3: After refmac, R = 0.3395 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 4: After refmac, R = 0.3254 (Rfree = 0.000) for 1164 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.3205 (Rfree = 0.000) for 1148 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.79 3.50 Search for helices and strands: 0 residues in 0 chains, 1213 seeds are put forward NCS extension: 0 residues added, 1213 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.364 Round 2: 90 peptides, 12 chains. Longest chain 11 peptides. Score 0.489 Round 3: 92 peptides, 13 chains. Longest chain 12 peptides. Score 0.473 Round 4: 94 peptides, 12 chains. Longest chain 16 peptides. Score 0.514 Round 5: 95 peptides, 11 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 5 Chains 11, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2621 restraints for refining 1198 atoms. 2296 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3299 (Rfree = 0.000) for 1198 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.3238 (Rfree = 0.000) for 1177 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.3168 (Rfree = 0.000) for 1156 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.2819 (Rfree = 0.000) for 1144 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.3112 (Rfree = 0.000) for 1139 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.57 Search for helices and strands: 0 residues in 0 chains, 1204 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1223 seeds are put forward Round 1: 92 peptides, 14 chains. Longest chain 10 peptides. Score 0.444 Round 2: 97 peptides, 13 chains. Longest chain 12 peptides. Score 0.505 Round 3: 98 peptides, 12 chains. Longest chain 18 peptides. Score 0.538 Round 4: 81 peptides, 12 chains. Longest chain 10 peptides. Score 0.430 Round 5: 83 peptides, 13 chains. Longest chain 8 peptides. Score 0.414 Taking the results from Round 3 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2510 restraints for refining 1197 atoms. 2152 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3285 (Rfree = 0.000) for 1197 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.3114 (Rfree = 0.000) for 1170 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 13: After refmac, R = 0.3060 (Rfree = 0.000) for 1152 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 14: After refmac, R = 0.3053 (Rfree = 0.000) for 1135 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.3155 (Rfree = 0.000) for 1128 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.53 Search for helices and strands: 0 residues in 0 chains, 1197 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1218 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.397 Round 2: 91 peptides, 13 chains. Longest chain 14 peptides. Score 0.467 Round 3: 86 peptides, 11 chains. Longest chain 11 peptides. Score 0.493 Round 4: 99 peptides, 13 chains. Longest chain 14 peptides. Score 0.517 Round 5: 87 peptides, 13 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 4 Chains 13, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2773 restraints for refining 1266 atoms. 2442 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3233 (Rfree = 0.000) for 1266 atoms. Found 5 (6 requested) and removed 15 (3 requested) atoms. Cycle 17: After refmac, R = 0.3276 (Rfree = 0.000) for 1231 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 18: After refmac, R = 0.3013 (Rfree = 0.000) for 1210 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 19: After refmac, R = 0.3028 (Rfree = 0.000) for 1196 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 20: After refmac, R = 0.3010 (Rfree = 0.000) for 1177 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 1244 seeds are put forward NCS extension: 0 residues added, 1244 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.326 Round 2: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.470 Round 3: 88 peptides, 10 chains. Longest chain 16 peptides. Score 0.533 Round 4: 86 peptides, 11 chains. Longest chain 15 peptides. Score 0.493 Round 5: 90 peptides, 12 chains. Longest chain 13 peptides. Score 0.489 Taking the results from Round 3 Chains 10, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2567 restraints for refining 1192 atoms. 2265 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3304 (Rfree = 0.000) for 1192 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 22: After refmac, R = 0.3181 (Rfree = 0.000) for 1174 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 23: After refmac, R = 0.3161 (Rfree = 0.000) for 1157 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.3113 (Rfree = 0.000) for 1147 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 25: After refmac, R = 0.2724 (Rfree = 0.000) for 1132 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 1198 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1217 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 11 peptides. Score 0.261 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.378 Round 3: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.393 Round 4: 79 peptides, 13 chains. Longest chain 8 peptides. Score 0.386 Round 5: 78 peptides, 11 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2834 restraints for refining 1249 atoms. 2577 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3269 (Rfree = 0.000) for 1249 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 27: After refmac, R = 0.3282 (Rfree = 0.000) for 1216 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 28: After refmac, R = 0.3196 (Rfree = 0.000) for 1192 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 29: After refmac, R = 0.3281 (Rfree = 0.000) for 1170 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.3245 (Rfree = 0.000) for 1159 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 1221 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1248 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.311 Round 2: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.393 Round 3: 81 peptides, 12 chains. Longest chain 11 peptides. Score 0.430 Round 4: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.414 Round 5: 87 peptides, 13 chains. Longest chain 11 peptides. Score 0.441 Taking the results from Round 5 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2614 restraints for refining 1196 atoms. 2331 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3317 (Rfree = 0.000) for 1196 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 32: After refmac, R = 0.3246 (Rfree = 0.000) for 1179 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 33: After refmac, R = 0.2978 (Rfree = 0.000) for 1154 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.3193 (Rfree = 0.000) for 1145 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.3278 (Rfree = 0.000) for 1140 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.52 Search for helices and strands: 0 residues in 0 chains, 1203 seeds are put forward NCS extension: 0 residues added, 1203 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.283 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.378 Round 3: 74 peptides, 12 chains. Longest chain 14 peptides. Score 0.381 Round 4: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.346 Round 5: 79 peptides, 12 chains. Longest chain 12 peptides. Score 0.417 Taking the results from Round 5 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2692 restraints for refining 1202 atoms. 2436 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3500 (Rfree = 0.000) for 1202 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.3505 (Rfree = 0.000) for 1175 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 38: After refmac, R = 0.3157 (Rfree = 0.000) for 1157 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.3480 (Rfree = 0.000) for 1147 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 40: After refmac, R = 0.3439 (Rfree = 0.000) for 1132 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.52 Search for helices and strands: 0 residues in 0 chains, 1190 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1207 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 11 peptides. Score 0.284 Round 2: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.339 Round 3: 80 peptides, 12 chains. Longest chain 15 peptides. Score 0.424 Round 4: 82 peptides, 13 chains. Longest chain 20 peptides. Score 0.407 Round 5: 81 peptides, 11 chains. Longest chain 21 peptides. Score 0.461 Taking the results from Round 5 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2661 reflections ( 99.18 % complete ) and 2432 restraints for refining 1137 atoms. 2163 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3598 (Rfree = 0.000) for 1137 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 42: After refmac, R = 0.3391 (Rfree = 0.000) for 1118 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.3521 (Rfree = 0.000) for 1108 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 44: After refmac, R = 0.3333 (Rfree = 0.000) for 1098 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.3305 (Rfree = 0.000) for 1094 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.54 Search for helices and strands: 0 residues in 0 chains, 1157 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1184 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.289 Round 2: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.377 Round 3: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.319 Round 4: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.403 Round 5: 76 peptides, 11 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 65, 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 2371 restraints for refining 1130 atoms. 2122 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3443 (Rfree = 0.000) for 1130 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3455 (Rfree = 0.000) for 1111 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3318 (Rfree = 0.000) for 1101 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3256 (Rfree = 0.000) for 1085 atoms. TimeTaking 31.07