Tue 25 Dec 19:27:58 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 2o7t-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.2-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/2o7t-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.2-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 ============================================================ Tue 25 Dec 19:28:06 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/2o7t-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.2-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: 0.6391 Checking the provided sequence file Detected sequence length: 199 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 199 Adjusted target solvent content: 0.45 Input MTZ file: 2o7t-3.2-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: 154 Cell parameters: 51.232 51.232 129.642 90.000 90.000 120.000 Input sequence file: 2o7t-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1592 target number of atoms Had to go as low as 0.65 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: 26.172 3.201 Wilson plot Bfac: 70.49 3557 reflections ( 99.75 % complete ) and 0 restraints for refining 1767 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3764 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3468 (Rfree = 0.000) for 1767 atoms. Found 11 (15 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1796 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.268 Round 2: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.371 Round 3: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.368 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.365 Round 5: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.345 Taking the results from Round 2 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 3603 restraints for refining 1453 atoms. 3398 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3312 (Rfree = 0.000) for 1453 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 2: After refmac, R = 0.3360 (Rfree = 0.000) for 1443 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.3093 (Rfree = 0.000) for 1434 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.3211 (Rfree = 0.000) for 1438 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.3213 (Rfree = 0.000) for 1432 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 1480 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 9 peptides. Score 0.249 Round 2: 74 peptides, 15 chains. Longest chain 10 peptides. Score 0.299 Round 3: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.383 Round 4: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.397 Round 5: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 5 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2898 restraints for refining 1280 atoms. 2614 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3252 (Rfree = 0.000) for 1280 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.3379 (Rfree = 0.000) for 1266 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.3478 (Rfree = 0.000) for 1262 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 9: After refmac, R = 0.3049 (Rfree = 0.000) for 1251 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.3119 (Rfree = 0.000) for 1248 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 3.23 Search for helices and strands: 0 residues in 0 chains, 1319 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.281 Round 2: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.418 Round 3: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.350 Round 4: 91 peptides, 15 chains. Longest chain 14 peptides. Score 0.441 Round 5: 91 peptides, 16 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 4 Chains 15, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2644 restraints for refining 1229 atoms. 2355 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3687 (Rfree = 0.000) for 1229 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.3493 (Rfree = 0.000) for 1220 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.3451 (Rfree = 0.000) for 1219 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.3414 (Rfree = 0.000) for 1213 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.3455 (Rfree = 0.000) for 1208 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 1281 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.281 Round 2: 88 peptides, 17 chains. Longest chain 7 peptides. Score 0.348 Round 3: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.456 Round 4: 85 peptides, 13 chains. Longest chain 13 peptides. Score 0.462 Round 5: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.439 Taking the results from Round 4 Chains 13, Residues 72, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3557 reflections ( 99.75 % complete ) and 2501 restraints for refining 1219 atoms. 2175 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3503 (Rfree = 0.000) for 1219 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 17: After refmac, R = 0.3461 (Rfree = 0.000) for 1204 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.3553 (Rfree = 0.000) for 1199 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.3450 (Rfree = 0.000) for 1194 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.3455 (Rfree = 0.000) for 1190 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.63 Search for helices and strands: 0 residues in 0 chains, 1259 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 6 peptides. Score 0.208 Round 2: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.270 Round 3: 87 peptides, 15 chains. Longest chain 9 peptides. Score 0.410 Round 4: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.412 Round 5: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.382 Taking the results from Round 4 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2652 restraints for refining 1220 atoms. 2390 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3262 (Rfree = 0.000) for 1220 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 22: After refmac, R = 0.3211 (Rfree = 0.000) for 1213 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.3343 (Rfree = 0.000) for 1206 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.3447 (Rfree = 0.000) for 1203 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.3101 (Rfree = 0.000) for 1202 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 1279 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 6 peptides. Score 0.236 Round 2: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.287 Round 3: 80 peptides, 16 chains. Longest chain 7 peptides. Score 0.315 Round 4: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.296 Round 5: 83 peptides, 17 chains. Longest chain 7 peptides. Score 0.305 Taking the results from Round 3 Chains 16, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2539 restraints for refining 1175 atoms. 2299 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3265 (Rfree = 0.000) for 1175 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.3188 (Rfree = 0.000) for 1173 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.3253 (Rfree = 0.000) for 1168 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 29: After refmac, R = 0.3056 (Rfree = 0.000) for 1163 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.3208 (Rfree = 0.000) for 1163 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 1236 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.230 Round 2: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.281 Round 3: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.308 Round 4: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.308 Round 5: 77 peptides, 15 chains. Longest chain 7 peptides. Score 0.326 Taking the results from Round 5 Chains 15, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2434 restraints for refining 1140 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3276 (Rfree = 0.000) for 1140 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2973 (Rfree = 0.000) for 1137 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2811 (Rfree = 0.000) for 1140 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.2884 (Rfree = 0.000) for 1139 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2734 (Rfree = 0.000) for 1138 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 1196 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 11 peptides. Score 0.326 Round 2: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.399 Round 3: 88 peptides, 16 chains. Longest chain 7 peptides. Score 0.383 Round 4: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.348 Round 5: 86 peptides, 15 chains. Longest chain 8 peptides. Score 0.402 Taking the results from Round 5 Chains 15, Residues 71, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2586 restraints for refining 1230 atoms. 2304 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3284 (Rfree = 0.000) for 1230 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 37: After refmac, R = 0.3577 (Rfree = 0.000) for 1217 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.3515 (Rfree = 0.000) for 1209 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.3172 (Rfree = 0.000) for 1199 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.3212 (Rfree = 0.000) for 1193 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 1271 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.285 Round 2: 69 peptides, 14 chains. Longest chain 6 peptides. Score 0.292 Round 3: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.298 Round 4: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.281 Round 5: 68 peptides, 14 chains. Longest chain 6 peptides. Score 0.283 Taking the results from Round 3 Chains 16, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3557 reflections ( 99.75 % complete ) and 2496 restraints for refining 1187 atoms. 2264 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3374 (Rfree = 0.000) for 1187 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.3282 (Rfree = 0.000) for 1184 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.3267 (Rfree = 0.000) for 1179 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.3292 (Rfree = 0.000) for 1176 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.3541 (Rfree = 0.000) for 1179 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 1253 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.198 Round 2: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.280 Round 3: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.336 Round 4: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.345 Round 5: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 53, 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 2o7t-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3557 reflections ( 99.75 % complete ) and 2626 restraints for refining 1197 atoms. 2425 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3450 (Rfree = 0.000) for 1197 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3391 (Rfree = 0.000) for 1186 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3138 (Rfree = 0.000) for 1178 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3146 (Rfree = 0.000) for 1173 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:08:41 GMT 2018 Job finished. TimeTaking 40.72