Sun 23 Dec 22:23:10 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 2fg9-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.6-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/2fg9-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.6-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 22:23:20 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/2fg9-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.6-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 125 and 0 Target number of residues in the AU: 125 Target solvent content: 0.6626 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: 2fg9-3.6-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: 211 Cell parameters: 134.000 134.000 134.000 90.000 90.000 90.000 Input sequence file: 2fg9-3.6-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 3.602 Wilson plot Bfac: 85.79 2578 reflections ( 99.54 % complete ) and 0 restraints for refining 1582 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3448 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3442 (Rfree = 0.000) for 1582 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 1583 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.346 Round 2: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.453 Round 3: 106 peptides, 12 chains. Longest chain 23 peptides. Score 0.627 Round 4: 110 peptides, 13 chains. Longest chain 26 peptides. Score 0.624 Round 5: 117 peptides, 12 chains. Longest chain 27 peptides. Score 0.685 Taking the results from Round 5 Chains 12, Residues 105, Estimated correctness of the model 44.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2781 restraints for refining 1291 atoms. 2373 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2796 (Rfree = 0.000) for 1291 atoms. Found 5 (8 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.2781 (Rfree = 0.000) for 1256 atoms. Found 3 (8 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.2643 (Rfree = 0.000) for 1237 atoms. Found 3 (7 requested) and removed 9 (3 requested) atoms. Cycle 4: After refmac, R = 0.2367 (Rfree = 0.000) for 1226 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2576 (Rfree = 0.000) for 1214 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward Round 1: 101 peptides, 16 chains. Longest chain 17 peptides. Score 0.480 Round 2: 109 peptides, 15 chains. Longest chain 17 peptides. Score 0.564 Round 3: 106 peptides, 16 chains. Longest chain 20 peptides. Score 0.515 Round 4: 108 peptides, 13 chains. Longest chain 21 peptides. Score 0.612 Round 5: 113 peptides, 15 chains. Longest chain 18 peptides. Score 0.588 Taking the results from Round 4 Chains 13, Residues 95, Estimated correctness of the model 19.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2811 restraints for refining 1291 atoms. 2444 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2471 (Rfree = 0.000) for 1291 atoms. Found 4 (8 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.2391 (Rfree = 0.000) for 1263 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 8: After refmac, R = 0.2379 (Rfree = 0.000) for 1256 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2801 (Rfree = 0.000) for 1251 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2178 (Rfree = 0.000) for 1239 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.41 Search for helices and strands: 0 residues in 0 chains, 1294 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 13 peptides. Score 0.324 Round 2: 106 peptides, 13 chains. Longest chain 18 peptides. Score 0.600 Round 3: 103 peptides, 15 chains. Longest chain 23 peptides. Score 0.524 Round 4: 100 peptides, 13 chains. Longest chain 23 peptides. Score 0.563 Round 5: 105 peptides, 13 chains. Longest chain 22 peptides. Score 0.594 Taking the results from Round 2 Chains 13, Residues 93, Estimated correctness of the model 14.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2799 restraints for refining 1284 atoms. 2440 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2327 (Rfree = 0.000) for 1284 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2193 (Rfree = 0.000) for 1274 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2136 (Rfree = 0.000) for 1266 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2011 (Rfree = 0.000) for 1259 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.1942 (Rfree = 0.000) for 1254 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 1306 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 12 peptides. Score 0.372 Round 2: 88 peptides, 14 chains. Longest chain 18 peptides. Score 0.448 Round 3: 96 peptides, 16 chains. Longest chain 13 peptides. Score 0.443 Round 4: 86 peptides, 13 chains. Longest chain 12 peptides. Score 0.466 Round 5: 97 peptides, 15 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 5 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2955 restraints for refining 1291 atoms. 2642 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2492 (Rfree = 0.000) for 1291 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 17: After refmac, R = 0.2265 (Rfree = 0.000) for 1289 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2133 (Rfree = 0.000) for 1280 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2108 (Rfree = 0.000) for 1274 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2060 (Rfree = 0.000) for 1268 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 1320 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Round 2: 88 peptides, 15 chains. Longest chain 14 peptides. Score 0.415 Round 3: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.451 Round 4: 78 peptides, 11 chains. Longest chain 11 peptides. Score 0.473 Round 5: 81 peptides, 12 chains. Longest chain 11 peptides. Score 0.462 Taking the results from Round 4 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 3036 restraints for refining 1291 atoms. 2779 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2378 (Rfree = 0.000) for 1291 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2347 (Rfree = 0.000) for 1282 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2264 (Rfree = 0.000) for 1273 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2337 (Rfree = 0.000) for 1266 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2156 (Rfree = 0.000) for 1262 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1304 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.311 Round 2: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.399 Round 3: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.415 Round 4: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.422 Round 5: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 5 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2807 restraints for refining 1291 atoms. 2487 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2423 (Rfree = 0.000) for 1291 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.2352 (Rfree = 0.000) for 1278 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2377 (Rfree = 0.000) for 1263 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2393 (Rfree = 0.000) for 1256 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.2397 (Rfree = 0.000) for 1246 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 1304 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.248 Round 2: 84 peptides, 14 chains. Longest chain 15 peptides. Score 0.417 Round 3: 86 peptides, 13 chains. Longest chain 14 peptides. Score 0.466 Round 4: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.466 Round 5: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Taking the results from Round 4 Chains 13, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2834 restraints for refining 1291 atoms. 2555 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2269 (Rfree = 0.000) for 1291 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2030 (Rfree = 0.000) for 1283 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2004 (Rfree = 0.000) for 1278 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2012 (Rfree = 0.000) for 1276 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.1758 (Rfree = 0.000) for 1273 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 1315 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.308 Round 2: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.420 Round 3: 84 peptides, 13 chains. Longest chain 12 peptides. Score 0.451 Round 4: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.459 Round 5: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 5 Chains 13, Residues 72, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2578 reflections ( 99.54 % complete ) and 2812 restraints for refining 1291 atoms. 2501 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2325 (Rfree = 0.000) for 1291 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2252 (Rfree = 0.000) for 1282 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2084 (Rfree = 0.000) for 1278 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1872 (Rfree = 0.000) for 1273 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1957 (Rfree = 0.000) for 1266 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1304 seeds are put forward Round 1: 63 peptides, 15 chains. Longest chain 5 peptides. Score 0.196 Round 2: 80 peptides, 17 chains. Longest chain 7 peptides. Score 0.277 Round 3: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.278 Round 4: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.296 Round 5: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.317 Taking the results from Round 5 Chains 14, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2578 reflections ( 99.54 % complete ) and 3080 restraints for refining 1290 atoms. 2862 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2483 (Rfree = 0.000) for 1290 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2580 (Rfree = 0.000) for 1275 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2494 (Rfree = 0.000) for 1270 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2678 (Rfree = 0.000) for 1264 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2516 (Rfree = 0.000) for 1261 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1299 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.209 Round 2: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.295 Round 3: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.389 Round 4: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.346 Round 5: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, 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 2fg9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2578 reflections ( 99.54 % complete ) and 2926 restraints for refining 1249 atoms. 2724 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2908 (Rfree = 0.000) for 1249 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2587 (Rfree = 0.000) for 1237 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2327 (Rfree = 0.000) for 1233 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2259 (Rfree = 0.000) for 1227 atoms. TimeTaking 47.13