null Tue 25 Dec 19:27:57 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 2eth-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-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/2eth-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-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 ============================================================ Tue 25 Dec 19:28:07 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/2eth-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-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 235 and 0 Target number of residues in the AU: 235 Target solvent content: 0.6620 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.56 Input MTZ file: 2eth-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2464 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 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: 65.143 3.800 Wilson plot Bfac: 85.72 3696 reflections ( 98.14 % complete ) and 0 restraints for refining 2711 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3297 (Rfree = 0.000) for 2711 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 2755 seeds are put forward NCS extension: 0 residues added, 2755 seeds are put forward Round 1: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.358 Round 2: 151 peptides, 22 chains. Longest chain 14 peptides. Score 0.466 Round 3: 149 peptides, 22 chains. Longest chain 14 peptides. Score 0.458 Round 4: 163 peptides, 21 chains. Longest chain 14 peptides. Score 0.529 Round 5: 168 peptides, 19 chains. Longest chain 21 peptides. Score 0.579 Taking the results from Round 5 Chains 19, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4894 restraints for refining 2121 atoms. 4317 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2748 (Rfree = 0.000) for 2121 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.2464 (Rfree = 0.000) for 2083 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 2069 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2290 (Rfree = 0.000) for 2057 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2280 (Rfree = 0.000) for 2049 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.47 Search for helices and strands: 0 residues in 0 chains, 2147 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2155 seeds are put forward Round 1: 151 peptides, 24 chains. Longest chain 11 peptides. Score 0.430 Round 2: 162 peptides, 21 chains. Longest chain 12 peptides. Score 0.526 Round 3: 165 peptides, 21 chains. Longest chain 17 peptides. Score 0.537 Round 4: 156 peptides, 21 chains. Longest chain 14 peptides. Score 0.503 Round 5: 158 peptides, 22 chains. Longest chain 13 peptides. Score 0.494 Taking the results from Round 3 Chains 21, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4933 restraints for refining 2125 atoms. 4378 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2532 (Rfree = 0.000) for 2125 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.2302 (Rfree = 0.000) for 2112 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.2233 (Rfree = 0.000) for 2106 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2209 (Rfree = 0.000) for 2101 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2179 (Rfree = 0.000) for 2095 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.50 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 0 residues added, 2202 seeds are put forward Round 1: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.371 Round 2: 143 peptides, 20 chains. Longest chain 14 peptides. Score 0.470 Round 3: 151 peptides, 21 chains. Longest chain 13 peptides. Score 0.484 Round 4: 138 peptides, 21 chains. Longest chain 13 peptides. Score 0.431 Round 5: 150 peptides, 21 chains. Longest chain 14 peptides. Score 0.480 Taking the results from Round 3 Chains 21, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4843 restraints for refining 2114 atoms. 4344 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2568 (Rfree = 0.000) for 2114 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2310 (Rfree = 0.000) for 2108 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2271 (Rfree = 0.000) for 2106 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2180 (Rfree = 0.000) for 2105 atoms. Found 7 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2179 (Rfree = 0.000) for 2104 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.49 Search for helices and strands: 0 residues in 0 chains, 2216 seeds are put forward NCS extension: 0 residues added, 2216 seeds are put forward Round 1: 124 peptides, 19 chains. Longest chain 9 peptides. Score 0.410 Round 2: 143 peptides, 20 chains. Longest chain 13 peptides. Score 0.470 Round 3: 146 peptides, 19 chains. Longest chain 14 peptides. Score 0.500 Round 4: 149 peptides, 19 chains. Longest chain 20 peptides. Score 0.511 Round 5: 145 peptides, 18 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 5 Chains 18, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5015 restraints for refining 2179 atoms. 4525 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2418 (Rfree = 0.000) for 2179 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 17: After refmac, R = 0.2439 (Rfree = 0.000) for 2162 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2230 (Rfree = 0.000) for 2154 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2424 (Rfree = 0.000) for 2147 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2284 (Rfree = 0.000) for 2144 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.47 Search for helices and strands: 0 residues in 0 chains, 2233 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2260 seeds are put forward Round 1: 127 peptides, 22 chains. Longest chain 13 peptides. Score 0.364 Round 2: 133 peptides, 18 chains. Longest chain 13 peptides. Score 0.466 Round 3: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.397 Round 4: 144 peptides, 20 chains. Longest chain 15 peptides. Score 0.474 Round 5: 140 peptides, 20 chains. Longest chain 13 peptides. Score 0.458 Taking the results from Round 4 Chains 20, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5045 restraints for refining 2189 atoms. 4569 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2565 (Rfree = 0.000) for 2189 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2333 (Rfree = 0.000) for 2178 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.2532 (Rfree = 0.000) for 2164 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.1928 (Rfree = 0.000) for 2142 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2247 (Rfree = 0.000) for 2134 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.48 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward NCS extension: 0 residues added, 2232 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 9 peptides. Score 0.256 Round 2: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.370 Round 3: 138 peptides, 23 chains. Longest chain 14 peptides. Score 0.394 Round 4: 130 peptides, 21 chains. Longest chain 14 peptides. Score 0.397 Round 5: 135 peptides, 21 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5104 restraints for refining 2205 atoms. 4669 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2245 (Rfree = 0.000) for 2205 atoms. Found 4 (12 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.2272 (Rfree = 0.000) for 2174 atoms. Found 6 (12 requested) and removed 14 (6 requested) atoms. Cycle 28: After refmac, R = 0.2216 (Rfree = 0.000) for 2149 atoms. Found 0 (11 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2269 (Rfree = 0.000) for 2130 atoms. Found 5 (11 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.2170 (Rfree = 0.000) for 2108 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 2187 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2203 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 6 peptides. Score 0.247 Round 2: 106 peptides, 20 chains. Longest chain 7 peptides. Score 0.306 Round 3: 114 peptides, 21 chains. Longest chain 9 peptides. Score 0.324 Round 4: 117 peptides, 18 chains. Longest chain 10 peptides. Score 0.399 Round 5: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.344 Taking the results from Round 4 Chains 18, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5041 restraints for refining 2143 atoms. 4663 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2394 (Rfree = 0.000) for 2143 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2325 (Rfree = 0.000) for 2130 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2401 (Rfree = 0.000) for 2120 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.2340 (Rfree = 0.000) for 2111 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 35: After refmac, R = 0.2323 (Rfree = 0.000) for 2107 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.57 Search for helices and strands: 0 residues in 0 chains, 2205 seeds are put forward NCS extension: 0 residues added, 2205 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 6 peptides. Score 0.222 Round 2: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.349 Round 3: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.340 Round 4: 115 peptides, 19 chains. Longest chain 13 peptides. Score 0.369 Round 5: 121 peptides, 20 chains. Longest chain 8 peptides. Score 0.377 Taking the results from Round 5 Chains 20, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5124 restraints for refining 2183 atoms. 4740 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2292 (Rfree = 0.000) for 2183 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.2471 (Rfree = 0.000) for 2177 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2240 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.2281 (Rfree = 0.000) for 2165 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2391 (Rfree = 0.000) for 2152 atoms. Found 9 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 0 residues added, 2242 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.270 Round 2: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.323 Round 3: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.289 Round 4: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.316 Round 5: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 5 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5037 restraints for refining 2151 atoms. 4721 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2332 (Rfree = 0.000) for 2151 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.2300 (Rfree = 0.000) for 2139 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2473 (Rfree = 0.000) for 2135 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 2126 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.2444 (Rfree = 0.000) for 2112 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 0 residues added, 2215 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.198 Round 2: 84 peptides, 17 chains. Longest chain 9 peptides. Score 0.259 Round 3: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.291 Round 4: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.286 Round 5: 92 peptides, 18 chains. Longest chain 7 peptides. Score 0.279 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 73, 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 2eth-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3696 reflections ( 98.14 % complete ) and 4549 restraints for refining 2011 atoms. 4274 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2304 (Rfree = 0.000) for 2011 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2187 (Rfree = 0.000) for 1996 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2191 (Rfree = 0.000) for 1982 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2049 (Rfree = 0.000) for 1973 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:13:31 GMT 2018 Job finished. TimeTaking 45.57 Used memory is bytes: 7952792