null Sun 23 Dec 22:22:53 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o3l-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.6-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 22:23:03 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o3l-3.6-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 143 and 0 Target number of residues in the AU: 143 Target solvent content: 0.6473 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1360 target number of atoms Had to go as low as 0.85 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 3.601 Wilson plot Bfac: 75.94 2759 reflections ( 99.75 % complete ) and 0 restraints for refining 1503 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3532 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3212 (Rfree = 0.000) for 1503 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.08 Search for helices and strands: 0 residues in 0 chains, 1549 seeds are put forward NCS extension: 0 residues added, 1549 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.301 Round 2: 80 peptides, 12 chains. Longest chain 10 peptides. Score 0.436 Round 3: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.481 Round 4: 96 peptides, 14 chains. Longest chain 12 peptides. Score 0.485 Round 5: 95 peptides, 12 chains. Longest chain 24 peptides. Score 0.536 Taking the results from Round 5 Chains 12, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2842 restraints for refining 1223 atoms. 2522 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3088 (Rfree = 0.000) for 1223 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2820 (Rfree = 0.000) for 1194 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2678 (Rfree = 0.000) for 1188 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2590 (Rfree = 0.000) for 1181 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2574 (Rfree = 0.000) for 1174 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.13 Search for helices and strands: 0 residues in 0 chains, 1249 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 1286 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.285 Round 2: 93 peptides, 13 chains. Longest chain 15 peptides. Score 0.495 Round 3: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.420 Round 4: 94 peptides, 14 chains. Longest chain 10 peptides. Score 0.471 Round 5: 101 peptides, 16 chains. Longest chain 10 peptides. Score 0.459 Taking the results from Round 2 Chains 13, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2732 restraints for refining 1198 atoms. 2425 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2526 (Rfree = 0.000) for 1198 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 7: After refmac, R = 0.2297 (Rfree = 0.000) for 1193 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 1185 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2217 (Rfree = 0.000) for 1176 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2217 (Rfree = 0.000) for 1175 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.16 Search for helices and strands: 0 residues in 0 chains, 1248 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 1252 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.359 Round 2: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.408 Round 3: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.459 Round 4: 99 peptides, 13 chains. Longest chain 12 peptides. Score 0.533 Round 5: 89 peptides, 13 chains. Longest chain 19 peptides. Score 0.468 Taking the results from Round 4 Chains 13, Residues 86, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2716 restraints for refining 1233 atoms. 2364 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2641 (Rfree = 0.000) for 1233 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2421 (Rfree = 0.000) for 1220 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 13: After refmac, R = 0.2337 (Rfree = 0.000) for 1220 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2267 (Rfree = 0.000) for 1213 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2250 (Rfree = 0.000) for 1205 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.20 Search for helices and strands: 0 residues in 0 chains, 1254 seeds are put forward NCS extension: 0 residues added, 1254 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.389 Round 2: 92 peptides, 11 chains. Longest chain 21 peptides. Score 0.546 Round 3: 92 peptides, 13 chains. Longest chain 19 peptides. Score 0.488 Round 4: 97 peptides, 11 chains. Longest chain 22 peptides. Score 0.576 Round 5: 91 peptides, 12 chains. Longest chain 17 peptides. Score 0.511 Taking the results from Round 4 Chains 11, Residues 86, Estimated correctness of the model 5.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2714 restraints for refining 1233 atoms. 2381 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2526 (Rfree = 0.000) for 1233 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 17: After refmac, R = 0.2198 (Rfree = 0.000) for 1226 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 18: After refmac, R = 0.2125 (Rfree = 0.000) for 1224 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2179 (Rfree = 0.000) for 1221 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2134 (Rfree = 0.000) for 1218 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.12 Search for helices and strands: 0 residues in 0 chains, 1281 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 1314 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.343 Round 2: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.437 Round 3: 86 peptides, 13 chains. Longest chain 13 peptides. Score 0.447 Round 4: 91 peptides, 14 chains. Longest chain 11 peptides. Score 0.451 Round 5: 88 peptides, 11 chains. Longest chain 14 peptides. Score 0.521 Taking the results from Round 5 Chains 11, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2800 restraints for refining 1233 atoms. 2503 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2386 (Rfree = 0.000) for 1233 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2280 (Rfree = 0.000) for 1226 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.2182 (Rfree = 0.000) for 1226 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2206 (Rfree = 0.000) for 1223 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2152 (Rfree = 0.000) for 1222 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.13 Search for helices and strands: 0 residues in 0 chains, 1295 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1313 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.279 Round 2: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.418 Round 3: 83 peptides, 9 chains. Longest chain 14 peptides. Score 0.548 Round 4: 83 peptides, 12 chains. Longest chain 11 peptides. Score 0.457 Round 5: 86 peptides, 13 chains. Longest chain 12 peptides. Score 0.447 Taking the results from Round 3 Chains 9, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2788 restraints for refining 1233 atoms. 2501 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2367 (Rfree = 0.000) for 1233 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2278 (Rfree = 0.000) for 1230 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2243 (Rfree = 0.000) for 1229 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2197 (Rfree = 0.000) for 1232 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2130 (Rfree = 0.000) for 1231 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.14 Search for helices and strands: 0 residues in 0 chains, 1291 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1302 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.288 Round 2: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.406 Round 3: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.353 Round 4: 91 peptides, 13 chains. Longest chain 11 peptides. Score 0.481 Round 5: 85 peptides, 14 chains. Longest chain 15 peptides. Score 0.408 Taking the results from Round 4 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2733 restraints for refining 1233 atoms. 2434 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2446 (Rfree = 0.000) for 1233 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2195 (Rfree = 0.000) for 1221 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2125 (Rfree = 0.000) for 1215 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2123 (Rfree = 0.000) for 1210 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2086 (Rfree = 0.000) for 1206 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.14 Search for helices and strands: 0 residues in 0 chains, 1244 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1258 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.314 Round 2: 75 peptides, 12 chains. Longest chain 11 peptides. Score 0.399 Round 3: 79 peptides, 11 chains. Longest chain 14 peptides. Score 0.461 Round 4: 80 peptides, 14 chains. Longest chain 15 peptides. Score 0.371 Round 5: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.381 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 ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2848 restraints for refining 1233 atoms. 2587 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2321 (Rfree = 0.000) for 1233 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.2016 (Rfree = 0.000) for 1226 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.1958 (Rfree = 0.000) for 1222 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.1981 (Rfree = 0.000) for 1219 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1982 (Rfree = 0.000) for 1214 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.15 Search for helices and strands: 0 residues in 0 chains, 1253 seeds are put forward NCS extension: 0 residues added, 1253 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.280 Round 2: 56 peptides, 9 chains. Longest chain 10 peptides. Score 0.355 Round 3: 62 peptides, 9 chains. Longest chain 12 peptides. Score 0.403 Round 4: 79 peptides, 10 chains. Longest chain 16 peptides. Score 0.492 Round 5: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 4 Chains 10, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2759 reflections ( 99.75 % complete ) and 2863 restraints for refining 1231 atoms. 2597 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2360 (Rfree = 0.000) for 1231 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2129 (Rfree = 0.000) for 1221 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2119 (Rfree = 0.000) for 1220 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2009 (Rfree = 0.000) for 1219 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1969 (Rfree = 0.000) for 1218 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.15 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 1284 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.269 Round 2: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.353 Round 3: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.348 Round 4: 69 peptides, 11 chains. Longest chain 14 peptides. Score 0.387 Round 5: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.439 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 2o3l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2759 reflections ( 99.75 % complete ) and 2797 restraints for refining 1233 atoms. 2548 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2573 (Rfree = 0.000) for 1233 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2145 (Rfree = 0.000) for 1229 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2066 (Rfree = 0.000) for 1226 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2089 (Rfree = 0.000) for 1223 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:08 GMT 2018 Job finished. TimeTaking 27.26 Used memory is bytes: 2043472