Sun 23 Dec 22:23:13 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 2prx-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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 22:23:22 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/2prx-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-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 216 and 0 Target number of residues in the AU: 216 Target solvent content: 0.6024 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2560 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: 28.816 3.600 Wilson plot Bfac: 53.52 3298 reflections ( 99.61 % complete ) and 0 restraints for refining 2822 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3196 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3238 (Rfree = 0.000) for 2822 atoms. Found 18 (18 requested) and removed 78 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 2783 seeds are put forward NCS extension: 0 residues added, 2783 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.229 Round 2: 79 peptides, 18 chains. Longest chain 7 peptides. Score 0.216 Round 3: 91 peptides, 18 chains. Longest chain 12 peptides. Score 0.294 Round 4: 105 peptides, 22 chains. Longest chain 8 peptides. Score 0.276 Round 5: 110 peptides, 19 chains. Longest chain 9 peptides. Score 0.381 Taking the results from Round 5 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5632 restraints for refining 2286 atoms. 5287 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2625 (Rfree = 0.000) for 2286 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 2: After refmac, R = 0.2173 (Rfree = 0.000) for 2237 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 3: After refmac, R = 0.2093 (Rfree = 0.000) for 2222 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 4: After refmac, R = 0.1985 (Rfree = 0.000) for 2202 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2120 (Rfree = 0.000) for 2195 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 2244 seeds are put forward NCS extension: 0 residues added, 2244 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 6 peptides. Score 0.221 Round 2: 100 peptides, 20 chains. Longest chain 8 peptides. Score 0.297 Round 3: 107 peptides, 22 chains. Longest chain 8 peptides. Score 0.288 Round 4: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.308 Round 5: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 5 Chains 18, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5152 restraints for refining 2117 atoms. 4846 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1896 (Rfree = 0.000) for 2117 atoms. Found 6 (13 requested) and removed 45 (6 requested) atoms. Cycle 7: After refmac, R = 0.1918 (Rfree = 0.000) for 2074 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.1938 (Rfree = 0.000) for 2062 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 9: After refmac, R = 0.1442 (Rfree = 0.000) for 2058 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.1363 (Rfree = 0.000) for 2052 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 2092 seeds are put forward NCS extension: 0 residues added, 2092 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 7 peptides. Score 0.235 Round 2: 124 peptides, 25 chains. Longest chain 9 peptides. Score 0.315 Round 3: 120 peptides, 24 chains. Longest chain 8 peptides. Score 0.316 Round 4: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.348 Round 5: 139 peptides, 25 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Chains 25, Residues 114, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 4503 restraints for refining 2062 atoms. 4019 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1729 (Rfree = 0.000) for 2062 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.1681 (Rfree = 0.000) for 2040 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 13: After refmac, R = 0.1704 (Rfree = 0.000) for 2027 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.1646 (Rfree = 0.000) for 2022 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 15: After refmac, R = 0.1579 (Rfree = 0.000) for 2015 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 0 residues added, 2060 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.340 Round 2: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.416 Round 3: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.449 Round 4: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.377 Round 5: 122 peptides, 19 chains. Longest chain 12 peptides. Score 0.446 Taking the results from Round 3 Chains 23, Residues 117, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 4755 restraints for refining 2114 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1612 (Rfree = 0.000) for 2114 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.1438 (Rfree = 0.000) for 2107 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.1358 (Rfree = 0.000) for 2096 atoms. Found 1 (13 requested) and removed 12 (6 requested) atoms. Cycle 19: After refmac, R = 0.1354 (Rfree = 0.000) for 2083 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1333 (Rfree = 0.000) for 2080 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward NCS extension: 0 residues added, 2117 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 8 peptides. Score 0.280 Round 2: 131 peptides, 21 chains. Longest chain 12 peptides. Score 0.447 Round 3: 134 peptides, 21 chains. Longest chain 14 peptides. Score 0.463 Round 4: 117 peptides, 21 chains. Longest chain 11 peptides. Score 0.372 Round 5: 125 peptides, 20 chains. Longest chain 10 peptides. Score 0.439 Taking the results from Round 3 Chains 21, Residues 113, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5159 restraints for refining 2220 atoms. 4709 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1473 (Rfree = 0.000) for 2220 atoms. Found 12 (14 requested) and removed 22 (7 requested) atoms. Cycle 22: After refmac, R = 0.1589 (Rfree = 0.000) for 2204 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.1312 (Rfree = 0.000) for 2199 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.1365 (Rfree = 0.000) for 2199 atoms. Found 6 (14 requested) and removed 15 (7 requested) atoms. Cycle 25: After refmac, R = 0.1150 (Rfree = 0.000) for 2188 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2250 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 8 peptides. Score 0.282 Round 2: 115 peptides, 21 chains. Longest chain 13 peptides. Score 0.360 Round 3: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.373 Round 4: 123 peptides, 22 chains. Longest chain 13 peptides. Score 0.381 Round 5: 126 peptides, 19 chains. Longest chain 14 peptides. Score 0.467 Taking the results from Round 5 Chains 19, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5329 restraints for refining 2280 atoms. 4920 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1479 (Rfree = 0.000) for 2280 atoms. Found 9 (14 requested) and removed 20 (7 requested) atoms. Cycle 27: After refmac, R = 0.1436 (Rfree = 0.000) for 2264 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.1366 (Rfree = 0.000) for 2257 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.1491 (Rfree = 0.000) for 2260 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1456 (Rfree = 0.000) for 2263 atoms. Found 12 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 2300 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 2321 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 7 peptides. Score 0.253 Round 2: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.336 Round 3: 102 peptides, 19 chains. Longest chain 10 peptides. Score 0.335 Round 4: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.346 Round 5: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 5 Chains 20, Residues 90, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5466 restraints for refining 2321 atoms. 5099 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1467 (Rfree = 0.000) for 2321 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 32: After refmac, R = 0.1378 (Rfree = 0.000) for 2307 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1553 (Rfree = 0.000) for 2307 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 34: After refmac, R = 0.1397 (Rfree = 0.000) for 2306 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1536 (Rfree = 0.000) for 2306 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 2357 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 2369 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.284 Round 2: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.368 Round 3: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.332 Round 4: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.346 Round 5: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.336 Taking the results from Round 2 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5427 restraints for refining 2321 atoms. 5071 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1458 (Rfree = 0.000) for 2321 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 37: After refmac, R = 0.1589 (Rfree = 0.000) for 2320 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 38: After refmac, R = 0.1489 (Rfree = 0.000) for 2317 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.1595 (Rfree = 0.000) for 2314 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.1123 (Rfree = 0.000) for 2307 atoms. Found 9 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 2344 seeds are put forward NCS extension: 0 residues added, 2344 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 7 peptides. Score 0.223 Round 2: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.330 Round 3: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.355 Round 4: 85 peptides, 14 chains. Longest chain 9 peptides. Score 0.363 Round 5: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 4 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3298 reflections ( 99.61 % complete ) and 5514 restraints for refining 2279 atoms. 5244 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1427 (Rfree = 0.000) for 2279 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 42: After refmac, R = 0.1205 (Rfree = 0.000) for 2277 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.1111 (Rfree = 0.000) for 2271 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1124 (Rfree = 0.000) for 2267 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1156 (Rfree = 0.000) for 2260 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 2291 seeds are put forward NCS extension: 0 residues added, 2291 seeds are put forward Round 1: 90 peptides, 21 chains. Longest chain 7 peptides. Score 0.207 Round 2: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.343 Round 3: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.321 Round 4: 95 peptides, 19 chains. Longest chain 9 peptides. Score 0.292 Round 5: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.322 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 91, 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 2prx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3298 reflections ( 99.61 % complete ) and 5281 restraints for refining 2236 atoms. 4938 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1430 (Rfree = 0.000) for 2236 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1583 (Rfree = 0.000) for 2223 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1447 (Rfree = 0.000) for 2211 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1511 (Rfree = 0.000) for 2201 atoms. TimeTaking 43.65