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 2o3l-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-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/2o3l-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-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 22:23:00 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/2o3l-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6671 Checking the provided sequence file Detected sequence length: 85 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 170 Adjusted target solvent content: 0.58 Input MTZ file: 2o3l-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: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1360 target number of atoms Had to go as low as 0.90 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: 52.947 4.001 Wilson plot Bfac: 89.12 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2050 reflections ( 99.66 % complete ) and 0 restraints for refining 1504 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3717 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3802 (Rfree = 0.000) for 1504 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 3.42 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward NCS extension: 0 residues added, 1523 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.249 Round 2: 63 peptides, 10 chains. Longest chain 13 peptides. Score 0.375 Round 3: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.403 Round 4: 74 peptides, 11 chains. Longest chain 16 peptides. Score 0.425 Round 5: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 5 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2721 restraints for refining 1170 atoms. 2483 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3098 (Rfree = 0.000) for 1170 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 2: After refmac, R = 0.2966 (Rfree = 0.000) for 1144 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 3: After refmac, R = 0.2865 (Rfree = 0.000) for 1128 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 4: After refmac, R = 0.2480 (Rfree = 0.000) for 1114 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2434 (Rfree = 0.000) for 1108 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.33 Search for helices and strands: 0 residues in 0 chains, 1167 seeds are put forward NCS extension: 0 residues added, 1167 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 12 peptides. Score 0.304 Round 2: 82 peptides, 13 chains. Longest chain 14 peptides. Score 0.418 Round 3: 84 peptides, 11 chains. Longest chain 15 peptides. Score 0.495 Round 4: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.461 Round 5: 80 peptides, 9 chains. Longest chain 14 peptides. Score 0.529 Taking the results from Round 5 Chains 9, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2675 restraints for refining 1197 atoms. 2400 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2843 (Rfree = 0.000) for 1197 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.2659 (Rfree = 0.000) for 1179 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 8: After refmac, R = 0.2380 (Rfree = 0.000) for 1167 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2267 (Rfree = 0.000) for 1162 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2226 (Rfree = 0.000) for 1163 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.39 Search for helices and strands: 0 residues in 0 chains, 1239 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1258 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.342 Round 2: 76 peptides, 9 chains. Longest chain 19 peptides. Score 0.503 Round 3: 77 peptides, 10 chains. Longest chain 15 peptides. Score 0.478 Round 4: 73 peptides, 9 chains. Longest chain 15 peptides. Score 0.483 Round 5: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 2 Chains 9, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2634 restraints for refining 1183 atoms. 2375 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2134 (Rfree = 0.000) for 1183 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 12: After refmac, R = 0.2070 (Rfree = 0.000) for 1169 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.1901 (Rfree = 0.000) for 1165 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.1868 (Rfree = 0.000) for 1159 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.1716 (Rfree = 0.000) for 1151 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.37 Search for helices and strands: 0 residues in 0 chains, 1203 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1227 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.342 Round 2: 79 peptides, 12 chains. Longest chain 16 peptides. Score 0.429 Round 3: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.421 Round 4: 79 peptides, 11 chains. Longest chain 13 peptides. Score 0.461 Round 5: 83 peptides, 12 chains. Longest chain 12 peptides. Score 0.457 Taking the results from Round 4 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2622 restraints for refining 1205 atoms. 2361 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2307 (Rfree = 0.000) for 1205 atoms. Found 4 (5 requested) and removed 10 (2 requested) atoms. Cycle 17: After refmac, R = 0.2349 (Rfree = 0.000) for 1187 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 18: After refmac, R = 0.2579 (Rfree = 0.000) for 1180 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 19: After refmac, R = 0.2330 (Rfree = 0.000) for 1172 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 20: After refmac, R = 0.2001 (Rfree = 0.000) for 1165 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.32 Search for helices and strands: 0 residues in 0 chains, 1242 seeds are put forward NCS extension: 0 residues added, 1242 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.295 Round 2: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.363 Round 3: 83 peptides, 14 chains. Longest chain 13 peptides. Score 0.393 Round 4: 84 peptides, 13 chains. Longest chain 15 peptides. Score 0.433 Round 5: 89 peptides, 15 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 4 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2665 restraints for refining 1216 atoms. 2394 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2383 (Rfree = 0.000) for 1216 atoms. Found 4 (5 requested) and removed 12 (2 requested) atoms. Cycle 22: After refmac, R = 0.2239 (Rfree = 0.000) for 1199 atoms. Found 1 (5 requested) and removed 10 (2 requested) atoms. Cycle 23: After refmac, R = 0.2501 (Rfree = 0.000) for 1188 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 24: After refmac, R = 0.2253 (Rfree = 0.000) for 1179 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 25: After refmac, R = 0.2444 (Rfree = 0.000) for 1171 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 1238 seeds are put forward NCS extension: 0 residues added, 1238 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.289 Round 2: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.347 Round 3: 69 peptides, 12 chains. Longest chain 13 peptides. Score 0.353 Round 4: 85 peptides, 14 chains. Longest chain 15 peptides. Score 0.408 Round 5: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 4 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2701 restraints for refining 1228 atoms. 2431 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2597 (Rfree = 0.000) for 1228 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 27: After refmac, R = 0.2293 (Rfree = 0.000) for 1212 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 28: After refmac, R = 0.1991 (Rfree = 0.000) for 1206 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 29: After refmac, R = 0.2114 (Rfree = 0.000) for 1196 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 30: After refmac, R = 0.2005 (Rfree = 0.000) for 1190 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.39 Search for helices and strands: 0 residues in 0 chains, 1265 seeds are put forward NCS extension: 0 residues added, 1265 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.276 Round 2: 67 peptides, 10 chains. Longest chain 15 peptides. Score 0.406 Round 3: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.436 Round 4: 81 peptides, 11 chains. Longest chain 16 peptides. Score 0.475 Round 5: 79 peptides, 11 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 4 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2714 restraints for refining 1227 atoms. 2445 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2195 (Rfree = 0.000) for 1227 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 32: After refmac, R = 0.2236 (Rfree = 0.000) for 1221 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2269 (Rfree = 0.000) for 1219 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.2120 (Rfree = 0.000) for 1213 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 35: After refmac, R = 0.2141 (Rfree = 0.000) for 1206 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 1275 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1299 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.259 Round 2: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.358 Round 3: 68 peptides, 13 chains. Longest chain 10 peptides. Score 0.310 Round 4: 68 peptides, 13 chains. Longest chain 10 peptides. Score 0.310 Round 5: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.345 Taking the results from Round 2 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2681 restraints for refining 1228 atoms. 2427 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2322 (Rfree = 0.000) for 1228 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 37: After refmac, R = 0.2196 (Rfree = 0.000) for 1223 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.2367 (Rfree = 0.000) for 1215 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 39: After refmac, R = 0.2274 (Rfree = 0.000) for 1207 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 40: After refmac, R = 0.2200 (Rfree = 0.000) for 1203 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.28 Search for helices and strands: 0 residues in 0 chains, 1258 seeds are put forward NCS extension: 0 residues added, 1258 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.221 Round 2: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.378 Round 3: 79 peptides, 11 chains. Longest chain 13 peptides. Score 0.461 Round 4: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.332 Round 5: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 3 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2050 reflections ( 99.66 % complete ) and 2721 restraints for refining 1228 atoms. 2460 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2357 (Rfree = 0.000) for 1228 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.2223 (Rfree = 0.000) for 1219 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.2194 (Rfree = 0.000) for 1216 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 44: After refmac, R = 0.2276 (Rfree = 0.000) for 1209 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.2304 (Rfree = 0.000) for 1206 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.39 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward NCS extension: 0 residues added, 1272 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.214 Round 2: 62 peptides, 10 chains. Longest chain 13 peptides. Score 0.367 Round 3: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.320 Round 4: 72 peptides, 11 chains. Longest chain 14 peptides. Score 0.410 Round 5: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 58, 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 2o3l-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2050 reflections ( 99.66 % complete ) and 2767 restraints for refining 1228 atoms. 2545 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2820 (Rfree = 0.000) for 1228 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2187 (Rfree = 0.000) for 1219 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2490 (Rfree = 0.000) for 1211 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2241 (Rfree = 0.000) for 1207 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:50 GMT 2018 Job finished. TimeTaking 25.97 Used memory is bytes: 7362552