Sun 23 Dec 22:23:02 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 2hh6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.4-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/2hh6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.4-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 22:23:12 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/2hh6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.4-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.6376 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.58 Input MTZ file: 2hh6-3.4-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: 179 Cell parameters: 93.536 93.536 115.318 90.000 90.000 120.000 Input sequence file: 2hh6-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 target number of atoms Had to go as low as 0.55 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: 81.005 3.400 Wilson plot Bfac: 69.73 4449 reflections ( 99.62 % complete ) and 0 restraints for refining 1996 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3294 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3885 (Rfree = 0.000) for 1996 atoms. Found 15 (15 requested) and removed 68 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 2.92 Search for helices and strands: 0 residues in 0 chains, 1974 seeds are put forward NCS extension: 0 residues added, 1974 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.235 Round 2: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.355 Round 3: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.405 Round 4: 92 peptides, 13 chains. Longest chain 15 peptides. Score 0.430 Round 5: 90 peptides, 13 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 4 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 3568 restraints for refining 1567 atoms. 3239 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3365 (Rfree = 0.000) for 1567 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 2: After refmac, R = 0.3253 (Rfree = 0.000) for 1490 atoms. Found 11 (11 requested) and removed 39 (5 requested) atoms. Cycle 3: After refmac, R = 0.3033 (Rfree = 0.000) for 1432 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 4: After refmac, R = 0.3496 (Rfree = 0.000) for 1392 atoms. Found 10 (10 requested) and removed 31 (5 requested) atoms. Cycle 5: After refmac, R = 0.2954 (Rfree = 0.000) for 1360 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1405 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1408 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.302 Round 2: 101 peptides, 15 chains. Longest chain 12 peptides. Score 0.430 Round 3: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.400 Round 4: 94 peptides, 14 chains. Longest chain 12 peptides. Score 0.416 Round 5: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 2 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2701 restraints for refining 1294 atoms. 2351 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2728 (Rfree = 0.000) for 1294 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2662 (Rfree = 0.000) for 1263 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.3472 (Rfree = 0.000) for 1241 atoms. Found 9 (9 requested) and removed 38 (4 requested) atoms. Cycle 9: After refmac, R = 0.3080 (Rfree = 0.000) for 1201 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.3139 (Rfree = 0.000) for 1187 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.21 Search for helices and strands: 0 residues in 0 chains, 1213 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1216 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.319 Round 2: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.411 Round 3: 92 peptides, 14 chains. Longest chain 11 peptides. Score 0.405 Round 4: 89 peptides, 14 chains. Longest chain 15 peptides. Score 0.388 Round 5: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 2 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2562 restraints for refining 1209 atoms. 2260 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3102 (Rfree = 0.000) for 1209 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.3148 (Rfree = 0.000) for 1188 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 13: After refmac, R = 0.2759 (Rfree = 0.000) for 1166 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2955 (Rfree = 0.000) for 1159 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2787 (Rfree = 0.000) for 1150 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 1209 seeds are put forward NCS extension: 0 residues added, 1209 seeds are put forward Round 1: 76 peptides, 14 chains. Longest chain 12 peptides. Score 0.308 Round 2: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.383 Round 3: 99 peptides, 16 chains. Longest chain 14 peptides. Score 0.394 Round 4: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.414 Round 5: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 4 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2764 restraints for refining 1269 atoms. 2421 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2785 (Rfree = 0.000) for 1269 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 17: After refmac, R = 0.2555 (Rfree = 0.000) for 1254 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.2358 (Rfree = 0.000) for 1244 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2597 (Rfree = 0.000) for 1239 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2202 (Rfree = 0.000) for 1236 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.92 Search for helices and strands: 0 residues in 0 chains, 1297 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 1307 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.317 Round 2: 100 peptides, 14 chains. Longest chain 12 peptides. Score 0.449 Round 3: 100 peptides, 16 chains. Longest chain 13 peptides. Score 0.400 Round 4: 101 peptides, 13 chains. Longest chain 21 peptides. Score 0.479 Round 5: 105 peptides, 14 chains. Longest chain 12 peptides. Score 0.475 Taking the results from Round 4 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2761 restraints for refining 1330 atoms. 2390 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2557 (Rfree = 0.000) for 1330 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 22: After refmac, R = 0.3229 (Rfree = 0.000) for 1307 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 23: After refmac, R = 0.2791 (Rfree = 0.000) for 1279 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.2848 (Rfree = 0.000) for 1264 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 25: After refmac, R = 0.2685 (Rfree = 0.000) for 1253 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 2.93 Search for helices and strands: 0 residues in 0 chains, 1322 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1335 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 10 peptides. Score 0.294 Round 2: 99 peptides, 14 chains. Longest chain 11 peptides. Score 0.444 Round 3: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.394 Round 4: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.446 Round 5: 104 peptides, 14 chains. Longest chain 14 peptides. Score 0.470 Taking the results from Round 5 Chains 14, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2873 restraints for refining 1369 atoms. 2527 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2573 (Rfree = 0.000) for 1369 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 27: After refmac, R = 0.2508 (Rfree = 0.000) for 1343 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2461 (Rfree = 0.000) for 1328 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2376 (Rfree = 0.000) for 1321 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.2452 (Rfree = 0.000) for 1310 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.93 Search for helices and strands: 0 residues in 0 chains, 1343 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1361 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.252 Round 2: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.370 Round 3: 81 peptides, 13 chains. Longest chain 10 peptides. Score 0.367 Round 4: 84 peptides, 12 chains. Longest chain 11 peptides. Score 0.411 Round 5: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 4 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2895 restraints for refining 1336 atoms. 2619 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2474 (Rfree = 0.000) for 1336 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2354 (Rfree = 0.000) for 1318 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2769 (Rfree = 0.000) for 1306 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 34: After refmac, R = 0.2411 (Rfree = 0.000) for 1291 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.2494 (Rfree = 0.000) for 1287 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 2.93 Search for helices and strands: 0 residues in 0 chains, 1333 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 1337 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 13 peptides. Score 0.347 Round 2: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.397 Round 3: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.411 Round 4: 94 peptides, 13 chains. Longest chain 12 peptides. Score 0.441 Round 5: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.408 Taking the results from Round 4 Chains 13, Residues 81, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2751 restraints for refining 1325 atoms. 2413 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2433 (Rfree = 0.000) for 1325 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.3083 (Rfree = 0.000) for 1315 atoms. Found 9 (9 requested) and removed 28 (4 requested) atoms. Cycle 38: After refmac, R = 0.3004 (Rfree = 0.000) for 1289 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 39: After refmac, R = 0.2449 (Rfree = 0.000) for 1275 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 40: After refmac, R = 0.2713 (Rfree = 0.000) for 1269 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward NCS extension: 0 residues added, 1321 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.304 Round 2: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.341 Round 3: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.325 Round 4: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.365 Round 5: 88 peptides, 15 chains. Longest chain 8 peptides. Score 0.356 Taking the results from Round 4 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4449 reflections ( 99.62 % complete ) and 2892 restraints for refining 1346 atoms. 2596 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2399 (Rfree = 0.000) for 1346 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 42: After refmac, R = 0.2463 (Rfree = 0.000) for 1324 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 43: After refmac, R = 0.2293 (Rfree = 0.000) for 1310 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2265 (Rfree = 0.000) for 1303 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.2457 (Rfree = 0.000) for 1298 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.92 Search for helices and strands: 0 residues in 0 chains, 1341 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1347 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.257 Round 2: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.397 Round 3: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.373 Round 4: 92 peptides, 13 chains. Longest chain 17 peptides. Score 0.430 Round 5: 91 peptides, 11 chains. Longest chain 16 peptides. Score 0.475 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 80, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2hh6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4449 reflections ( 99.62 % complete ) and 2539 restraints for refining 1321 atoms. 2175 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2561 (Rfree = 0.000) for 1321 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2510 (Rfree = 0.000) for 1304 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2915 (Rfree = 0.000) for 1290 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2359 (Rfree = 0.000) for 1283 atoms. TimeTaking 33.97