Sun 23 Dec 22:23:05 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.4-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 22:23:15 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-3.4-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 128 and 0 Target number of residues in the AU: 128 Target solvent content: 0.6474 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1592 target number of atoms Had to go as low as 0.70 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 3.401 Wilson plot Bfac: 76.36 2974 reflections ( 99.70 % complete ) and 0 restraints for refining 1764 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3702 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3485 (Rfree = 0.000) for 1764 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.257 Round 2: 79 peptides, 16 chains. Longest chain 6 peptides. Score 0.307 Round 3: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.405 Round 4: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.375 Round 5: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.397 Taking the results from Round 3 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 3546 restraints for refining 1448 atoms. 3251 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2832 (Rfree = 0.000) for 1448 atoms. Found 3 (10 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.2573 (Rfree = 0.000) for 1404 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2575 (Rfree = 0.000) for 1383 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2831 (Rfree = 0.000) for 1364 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2469 (Rfree = 0.000) for 1349 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.251 Round 2: 80 peptides, 17 chains. Longest chain 6 peptides. Score 0.279 Round 3: 83 peptides, 17 chains. Longest chain 7 peptides. Score 0.305 Round 4: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.322 Round 5: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 5 Chains 17, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 2938 restraints for refining 1319 atoms. 2655 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2735 (Rfree = 0.000) for 1319 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 7: After refmac, R = 0.2542 (Rfree = 0.000) for 1298 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2470 (Rfree = 0.000) for 1290 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2265 (Rfree = 0.000) for 1283 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2415 (Rfree = 0.000) for 1276 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 1341 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.235 Round 2: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.379 Round 3: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.405 Round 4: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.439 Round 5: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.369 Taking the results from Round 4 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 2903 restraints for refining 1298 atoms. 2603 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2526 (Rfree = 0.000) for 1298 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2416 (Rfree = 0.000) for 1297 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.2311 (Rfree = 0.000) for 1295 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2163 (Rfree = 0.000) for 1292 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2158 (Rfree = 0.000) for 1290 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 1373 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.262 Round 2: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.367 Round 3: 84 peptides, 14 chains. Longest chain 8 peptides. Score 0.420 Round 4: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.423 Round 5: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.415 Taking the results from Round 4 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 2942 restraints for refining 1290 atoms. 2650 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2469 (Rfree = 0.000) for 1290 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2822 (Rfree = 0.000) for 1292 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2319 (Rfree = 0.000) for 1290 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2296 (Rfree = 0.000) for 1292 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2349 (Rfree = 0.000) for 1290 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 1365 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 8 peptides. Score 0.251 Round 2: 86 peptides, 15 chains. Longest chain 15 peptides. Score 0.402 Round 3: 86 peptides, 16 chains. Longest chain 8 peptides. Score 0.367 Round 4: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.289 Round 5: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.369 Taking the results from Round 2 Chains 15, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 2899 restraints for refining 1282 atoms. 2630 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2377 (Rfree = 0.000) for 1282 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 22: After refmac, R = 0.2333 (Rfree = 0.000) for 1277 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2216 (Rfree = 0.000) for 1281 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2157 (Rfree = 0.000) for 1282 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2371 (Rfree = 0.000) for 1278 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 1364 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.217 Round 2: 83 peptides, 16 chains. Longest chain 7 peptides. Score 0.341 Round 3: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.391 Round 4: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.415 Round 5: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 4 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 3038 restraints for refining 1345 atoms. 2750 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2411 (Rfree = 0.000) for 1345 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2214 (Rfree = 0.000) for 1343 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2170 (Rfree = 0.000) for 1336 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2132 (Rfree = 0.000) for 1333 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2110 (Rfree = 0.000) for 1336 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward Round 1: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.359 Round 2: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.428 Round 3: 84 peptides, 14 chains. Longest chain 15 peptides. Score 0.420 Round 4: 90 peptides, 15 chains. Longest chain 15 peptides. Score 0.433 Round 5: 87 peptides, 14 chains. Longest chain 15 peptides. Score 0.444 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 3107 restraints for refining 1383 atoms. 2829 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2353 (Rfree = 0.000) for 1383 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 32: After refmac, R = 0.2223 (Rfree = 0.000) for 1377 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2250 (Rfree = 0.000) for 1372 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2289 (Rfree = 0.000) for 1367 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2397 (Rfree = 0.000) for 1364 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 1428 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.260 Round 2: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.315 Round 3: 69 peptides, 12 chains. Longest chain 8 peptides. Score 0.368 Round 4: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.362 Round 5: 69 peptides, 11 chains. Longest chain 12 peptides. Score 0.405 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 3209 restraints for refining 1385 atoms. 2988 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2528 (Rfree = 0.000) for 1385 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 37: After refmac, R = 0.2571 (Rfree = 0.000) for 1375 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2147 (Rfree = 0.000) for 1371 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2041 (Rfree = 0.000) for 1364 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2022 (Rfree = 0.000) for 1358 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 1415 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 9 peptides. Score 0.289 Round 2: 51 peptides, 10 chains. Longest chain 9 peptides. Score 0.282 Round 3: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.311 Round 4: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.232 Round 5: 51 peptides, 10 chains. Longest chain 9 peptides. Score 0.282 Taking the results from Round 3 Chains 10, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 3183 restraints for refining 1334 atoms. 3017 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2267 (Rfree = 0.000) for 1334 atoms. Found 4 (10 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.2215 (Rfree = 0.000) for 1324 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2190 (Rfree = 0.000) for 1319 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.2234 (Rfree = 0.000) for 1318 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2125 (Rfree = 0.000) for 1317 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 1373 seeds are put forward Round 1: 29 peptides, 6 chains. Longest chain 9 peptides. Score 0.232 Round 2: 47 peptides, 9 chains. Longest chain 9 peptides. Score 0.285 Round 3: 50 peptides, 10 chains. Longest chain 9 peptides. Score 0.273 Round 4: 49 peptides, 11 chains. Longest chain 7 peptides. Score 0.220 Round 5: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.222 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 38, 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. 2974 reflections ( 99.70 % complete ) and 2933 restraints for refining 1280 atoms. 2790 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2556 (Rfree = 0.000) for 1280 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2697 (Rfree = 0.000) for 1275 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2556 (Rfree = 0.000) for 1268 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2604 (Rfree = 0.000) for 1263 atoms. TimeTaking 27.42