null Sun 23 Dec 22:22:49 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 2fg9-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.8-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/2fg9-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.8-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 22:22:59 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/2fg9-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.8-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 123 and 0 Target number of residues in the AU: 123 Target solvent content: 0.6680 Checking the provided sequence file Detected sequence length: 178 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 178 Adjusted target solvent content: 0.52 Input MTZ file: 2fg9-3.8-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: 211 Cell parameters: 134.000 134.000 134.000 90.000 90.000 90.000 Input sequence file: 2fg9-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1424 target number of atoms Had to go as low as 0.80 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: 94.752 3.802 Wilson plot Bfac: 89.89 2215 reflections ( 99.46 % complete ) and 0 restraints for refining 1572 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3447 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2892 (Rfree = 0.000) for 1572 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1593 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 13 peptides. Score 0.348 Round 2: 98 peptides, 13 chains. Longest chain 15 peptides. Score 0.550 Round 3: 106 peptides, 14 chains. Longest chain 14 peptides. Score 0.573 Round 4: 101 peptides, 13 chains. Longest chain 16 peptides. Score 0.570 Round 5: 112 peptides, 15 chains. Longest chain 17 peptides. Score 0.582 Taking the results from Round 5 Chains 15, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 2896 restraints for refining 1288 atoms. 2523 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2836 (Rfree = 0.000) for 1288 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.2715 (Rfree = 0.000) for 1254 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2524 (Rfree = 0.000) for 1241 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2509 (Rfree = 0.000) for 1240 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2431 (Rfree = 0.000) for 1232 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 1273 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.315 Round 2: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.451 Round 3: 110 peptides, 14 chains. Longest chain 15 peptides. Score 0.597 Round 4: 109 peptides, 16 chains. Longest chain 15 peptides. Score 0.535 Round 5: 110 peptides, 15 chains. Longest chain 11 peptides. Score 0.570 Taking the results from Round 3 Chains 14, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 2709 restraints for refining 1245 atoms. 2339 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2601 (Rfree = 0.000) for 1245 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.2449 (Rfree = 0.000) for 1229 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 8: After refmac, R = 0.2353 (Rfree = 0.000) for 1221 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2479 (Rfree = 0.000) for 1213 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.2500 (Rfree = 0.000) for 1204 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 1249 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 9 peptides. Score 0.418 Round 2: 91 peptides, 12 chains. Longest chain 12 peptides. Score 0.533 Round 3: 90 peptides, 13 chains. Longest chain 11 peptides. Score 0.495 Round 4: 90 peptides, 14 chains. Longest chain 12 peptides. Score 0.463 Round 5: 101 peptides, 13 chains. Longest chain 12 peptides. Score 0.570 Taking the results from Round 5 Chains 13, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 2892 restraints for refining 1288 atoms. 2553 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2614 (Rfree = 0.000) for 1288 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2576 (Rfree = 0.000) for 1264 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2268 (Rfree = 0.000) for 1253 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2702 (Rfree = 0.000) for 1244 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 15: After refmac, R = 0.2763 (Rfree = 0.000) for 1226 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1278 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 13 peptides. Score 0.331 Round 2: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.410 Round 3: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.443 Round 4: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Round 5: 93 peptides, 13 chains. Longest chain 14 peptides. Score 0.516 Taking the results from Round 5 Chains 13, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 2985 restraints for refining 1280 atoms. 2678 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2690 (Rfree = 0.000) for 1280 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2335 (Rfree = 0.000) for 1258 atoms. Found 4 (7 requested) and removed 10 (3 requested) atoms. Cycle 18: After refmac, R = 0.2231 (Rfree = 0.000) for 1246 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2118 (Rfree = 0.000) for 1234 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2204 (Rfree = 0.000) for 1227 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 1261 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.366 Round 2: 90 peptides, 14 chains. Longest chain 12 peptides. Score 0.463 Round 3: 99 peptides, 11 chains. Longest chain 15 peptides. Score 0.613 Round 4: 90 peptides, 11 chains. Longest chain 15 peptides. Score 0.557 Round 5: 97 peptides, 11 chains. Longest chain 20 peptides. Score 0.601 Taking the results from Round 3 Chains 11, Residues 88, Estimated correctness of the model 4.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 2874 restraints for refining 1288 atoms. 2533 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2691 (Rfree = 0.000) for 1288 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 1270 atoms. Found 3 (7 requested) and removed 21 (3 requested) atoms. Cycle 23: After refmac, R = 0.2239 (Rfree = 0.000) for 1249 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2233 (Rfree = 0.000) for 1240 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2216 (Rfree = 0.000) for 1238 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1277 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 10 peptides. Score 0.337 Round 2: 85 peptides, 12 chains. Longest chain 13 peptides. Score 0.491 Round 3: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.435 Round 4: 87 peptides, 11 chains. Longest chain 13 peptides. Score 0.537 Round 5: 82 peptides, 12 chains. Longest chain 11 peptides. Score 0.469 Taking the results from Round 4 Chains 11, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 2940 restraints for refining 1288 atoms. 2647 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2918 (Rfree = 0.000) for 1288 atoms. Found 1 (7 requested) and removed 11 (3 requested) atoms. Cycle 27: After refmac, R = 0.2507 (Rfree = 0.000) for 1270 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2261 (Rfree = 0.000) for 1259 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2263 (Rfree = 0.000) for 1255 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2206 (Rfree = 0.000) for 1248 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 1265 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 11 peptides. Score 0.311 Round 2: 57 peptides, 8 chains. Longest chain 12 peptides. Score 0.415 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.343 Round 4: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.394 Round 5: 74 peptides, 13 chains. Longest chain 17 peptides. Score 0.371 Taking the results from Round 2 Chains 8, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 3000 restraints for refining 1265 atoms. 2812 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2379 (Rfree = 0.000) for 1265 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2389 (Rfree = 0.000) for 1263 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.2139 (Rfree = 0.000) for 1266 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.1841 (Rfree = 0.000) for 1261 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1779 (Rfree = 0.000) for 1255 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1286 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 11 peptides. Score 0.269 Round 2: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.414 Round 3: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.422 Round 4: 62 peptides, 10 chains. Longest chain 9 peptides. Score 0.381 Round 5: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 3 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 3137 restraints for refining 1288 atoms. 2919 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2752 (Rfree = 0.000) for 1288 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.2244 (Rfree = 0.000) for 1280 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2134 (Rfree = 0.000) for 1274 atoms. Found 0 (7 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.1953 (Rfree = 0.000) for 1267 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.1942 (Rfree = 0.000) for 1262 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 1291 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 8 peptides. Score 0.228 Round 2: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.313 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.343 Round 4: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.377 Round 5: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.365 Taking the results from Round 4 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2215 reflections ( 99.46 % complete ) and 3082 restraints for refining 1286 atoms. 2873 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2239 (Rfree = 0.000) for 1286 atoms. Found 1 (7 requested) and removed 13 (3 requested) atoms. Cycle 42: After refmac, R = 0.2376 (Rfree = 0.000) for 1273 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.2081 (Rfree = 0.000) for 1267 atoms. Found 0 (6 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.1908 (Rfree = 0.000) for 1258 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2041 (Rfree = 0.000) for 1254 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 1294 seeds are put forward Round 1: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.178 Round 2: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.274 Round 3: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.322 Round 4: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.306 Round 5: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 48, 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 2fg9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2215 reflections ( 99.46 % complete ) and 3052 restraints for refining 1288 atoms. 2870 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2312 (Rfree = 0.000) for 1288 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2321 (Rfree = 0.000) for 1278 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2258 (Rfree = 0.000) for 1270 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2036 (Rfree = 0.000) for 1262 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:25 GMT 2018 Job finished. TimeTaking 45.59 Used memory is bytes: 12625592