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 2ozj-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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/2ozj-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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 22:23:02 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/2ozj-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6579 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.65 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: 75.275 3.800 Wilson plot Bfac: 83.46 2297 reflections ( 99.14 % complete ) and 0 restraints for refining 2013 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2737 (Rfree = 0.000) for 2013 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward NCS extension: 0 residues added, 2019 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.301 Round 2: 93 peptides, 13 chains. Longest chain 18 peptides. Score 0.499 Round 3: 114 peptides, 15 chains. Longest chain 20 peptides. Score 0.574 Round 4: 119 peptides, 16 chains. Longest chain 24 peptides. Score 0.577 Round 5: 107 peptides, 16 chains. Longest chain 13 peptides. Score 0.504 Taking the results from Round 4 Chains 17, Residues 103, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3661 restraints for refining 1650 atoms. 3224 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2622 (Rfree = 0.000) for 1650 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.2710 (Rfree = 0.000) for 1607 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2860 (Rfree = 0.000) for 1572 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 4: After refmac, R = 0.2790 (Rfree = 0.000) for 1542 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.2756 (Rfree = 0.000) for 1524 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 1568 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 1598 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 14 peptides. Score 0.376 Round 2: 84 peptides, 13 chains. Longest chain 15 peptides. Score 0.436 Round 3: 99 peptides, 15 chains. Longest chain 16 peptides. Score 0.480 Round 4: 96 peptides, 13 chains. Longest chain 16 peptides. Score 0.519 Round 5: 107 peptides, 16 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 4 Chains 13, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3151 restraints for refining 1421 atoms. 2832 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2697 (Rfree = 0.000) for 1421 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.3202 (Rfree = 0.000) for 1404 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.2533 (Rfree = 0.000) for 1386 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2225 (Rfree = 0.000) for 1383 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2197 (Rfree = 0.000) for 1376 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 1426 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1450 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.336 Round 2: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.367 Round 3: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.452 Round 4: 100 peptides, 15 chains. Longest chain 16 peptides. Score 0.487 Round 5: 99 peptides, 14 chains. Longest chain 14 peptides. Score 0.509 Taking the results from Round 5 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3187 restraints for refining 1429 atoms. 2861 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2762 (Rfree = 0.000) for 1429 atoms. Found 6 (7 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2680 (Rfree = 0.000) for 1408 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.2576 (Rfree = 0.000) for 1397 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2738 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2498 (Rfree = 0.000) for 1384 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward NCS extension: 0 residues added, 1413 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.301 Round 2: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.407 Round 3: 98 peptides, 14 chains. Longest chain 16 peptides. Score 0.503 Round 4: 97 peptides, 15 chains. Longest chain 17 peptides. Score 0.466 Round 5: 94 peptides, 14 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 3 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3089 restraints for refining 1364 atoms. 2767 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2563 (Rfree = 0.000) for 1364 atoms. Found 2 (7 requested) and removed 12 (3 requested) atoms. Cycle 17: After refmac, R = 0.2372 (Rfree = 0.000) for 1346 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.2279 (Rfree = 0.000) for 1334 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2485 (Rfree = 0.000) for 1328 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2208 (Rfree = 0.000) for 1327 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 1345 seeds are put forward NCS extension: 0 residues added, 1345 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 6 peptides. Score 0.220 Round 2: 99 peptides, 18 chains. Longest chain 13 peptides. Score 0.388 Round 3: 92 peptides, 17 chains. Longest chain 11 peptides. Score 0.367 Round 4: 111 peptides, 21 chains. Longest chain 8 peptides. Score 0.383 Round 5: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 5 Chains 20, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3046 restraints for refining 1377 atoms. 2706 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2473 (Rfree = 0.000) for 1377 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.2399 (Rfree = 0.000) for 1358 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2400 (Rfree = 0.000) for 1351 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.2279 (Rfree = 0.000) for 1345 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2125 (Rfree = 0.000) for 1343 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 1380 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 9 peptides. Score 0.248 Round 2: 77 peptides, 16 chains. Longest chain 9 peptides. Score 0.281 Round 3: 78 peptides, 12 chains. Longest chain 15 peptides. Score 0.425 Round 4: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.417 Round 5: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.404 Taking the results from Round 3 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3247 restraints for refining 1401 atoms. 2995 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2620 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2314 (Rfree = 0.000) for 1401 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2461 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2302 (Rfree = 0.000) for 1391 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.2292 (Rfree = 0.000) for 1384 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 1414 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1435 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.267 Round 2: 75 peptides, 12 chains. Longest chain 11 peptides. Score 0.402 Round 3: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.355 Round 4: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.323 Round 5: 77 peptides, 13 chains. Longest chain 9 peptides. Score 0.384 Taking the results from Round 2 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3291 restraints for refining 1410 atoms. 3051 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2174 (Rfree = 0.000) for 1410 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2047 (Rfree = 0.000) for 1406 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2059 (Rfree = 0.000) for 1402 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2477 (Rfree = 0.000) for 1396 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2131 (Rfree = 0.000) for 1395 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 1433 seeds are put forward NCS extension: 0 residues added, 1433 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.206 Round 2: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.306 Round 3: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.306 Round 4: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.297 Round 5: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.300 Taking the results from Round 3 Chains 12, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3169 restraints for refining 1367 atoms. 2977 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2265 (Rfree = 0.000) for 1367 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 37: After refmac, R = 0.2454 (Rfree = 0.000) for 1366 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2184 (Rfree = 0.000) for 1364 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2417 (Rfree = 0.000) for 1360 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 40: After refmac, R = 0.2165 (Rfree = 0.000) for 1355 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward NCS extension: 0 residues added, 1377 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 5 peptides. Score 0.225 Round 2: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.245 Round 3: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.288 Round 4: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.341 Round 5: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.300 Taking the results from Round 4 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2297 reflections ( 99.14 % complete ) and 3161 restraints for refining 1329 atoms. 2990 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2329 (Rfree = 0.000) for 1329 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2273 (Rfree = 0.000) for 1321 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2198 (Rfree = 0.000) for 1317 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2200 (Rfree = 0.000) for 1313 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2189 (Rfree = 0.000) for 1310 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 1333 seeds are put forward NCS extension: 0 residues added, 1333 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 6 peptides. Score 0.257 Round 2: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.280 Round 3: 62 peptides, 9 chains. Longest chain 11 peptides. Score 0.406 Round 4: 60 peptides, 10 chains. Longest chain 8 peptides. Score 0.354 Round 5: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, 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 2ozj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2297 reflections ( 99.14 % complete ) and 3046 restraints for refining 1333 atoms. 2843 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2226 (Rfree = 0.000) for 1333 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2381 (Rfree = 0.000) for 1329 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2425 (Rfree = 0.000) for 1322 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2119 (Rfree = 0.000) for 1319 atoms. TimeTaking 28.15