null Mon 24 Dec 07:31:17 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2eth-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:31:21 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/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.8-parrot-noncs/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-noncs.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-noncs.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 2737 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3424 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3243 (Rfree = 0.000) for 2737 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 0 residues added, 2794 seeds are put forward Round 1: 112 peptides, 20 chains. Longest chain 11 peptides. Score 0.335 Round 2: 147 peptides, 19 chains. Longest chain 16 peptides. Score 0.504 Round 3: 156 peptides, 20 chains. Longest chain 17 peptides. Score 0.520 Round 4: 146 peptides, 18 chains. Longest chain 19 peptides. Score 0.517 Round 5: 154 peptides, 17 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 17, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5234 restraints for refining 2228 atoms. 4703 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2720 (Rfree = 0.000) for 2228 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.2740 (Rfree = 0.000) for 2179 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 3: After refmac, R = 0.2652 (Rfree = 0.000) for 2144 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 4: After refmac, R = 0.2586 (Rfree = 0.000) for 2115 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 5: After refmac, R = 0.2484 (Rfree = 0.000) for 2099 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 2212 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2229 seeds are put forward Round 1: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.362 Round 2: 141 peptides, 21 chains. Longest chain 12 peptides. Score 0.444 Round 3: 151 peptides, 23 chains. Longest chain 13 peptides. Score 0.448 Round 4: 140 peptides, 23 chains. Longest chain 10 peptides. Score 0.402 Round 5: 152 peptides, 19 chains. Longest chain 20 peptides. Score 0.523 Taking the results from Round 5 Chains 19, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5152 restraints for refining 2210 atoms. 4639 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2449 (Rfree = 0.000) for 2210 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.2476 (Rfree = 0.000) for 2186 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.2431 (Rfree = 0.000) for 2169 atoms. Found 10 (12 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2270 (Rfree = 0.000) for 2149 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.2286 (Rfree = 0.000) for 2145 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 2258 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 2275 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 10 peptides. Score 0.302 Round 2: 132 peptides, 21 chains. Longest chain 13 peptides. Score 0.406 Round 3: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.421 Round 4: 146 peptides, 20 chains. Longest chain 20 peptides. Score 0.482 Round 5: 145 peptides, 20 chains. Longest chain 18 peptides. Score 0.478 Taking the results from Round 4 Chains 20, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5149 restraints for refining 2227 atoms. 4665 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2248 (Rfree = 0.000) for 2227 atoms. Found 11 (12 requested) and removed 15 (6 requested) atoms. Cycle 12: After refmac, R = 0.2327 (Rfree = 0.000) for 2194 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 13: After refmac, R = 0.2368 (Rfree = 0.000) for 2176 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.2318 (Rfree = 0.000) for 2157 atoms. Found 10 (11 requested) and removed 14 (5 requested) atoms. Cycle 15: After refmac, R = 0.2214 (Rfree = 0.000) for 2140 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 2281 seeds are put forward Round 1: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.350 Round 2: 138 peptides, 20 chains. Longest chain 19 peptides. Score 0.450 Round 3: 133 peptides, 20 chains. Longest chain 11 peptides. Score 0.429 Round 4: 133 peptides, 21 chains. Longest chain 10 peptides. Score 0.410 Round 5: 133 peptides, 19 chains. Longest chain 10 peptides. Score 0.448 Taking the results from Round 2 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4807 restraints for refining 2155 atoms. 4355 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2288 (Rfree = 0.000) for 2155 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2242 (Rfree = 0.000) for 2139 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2313 (Rfree = 0.000) for 2132 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2120 (Rfree = 0.000) for 2122 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2301 (Rfree = 0.000) for 2113 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2257 seeds are put forward Round 1: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.336 Round 2: 131 peptides, 20 chains. Longest chain 15 peptides. Score 0.420 Round 3: 135 peptides, 18 chains. Longest chain 20 peptides. Score 0.475 Round 4: 144 peptides, 20 chains. Longest chain 11 peptides. Score 0.474 Round 5: 133 peptides, 20 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 3 Chains 18, Residues 117, 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 2203 atoms. 4591 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2221 (Rfree = 0.000) for 2203 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.2308 (Rfree = 0.000) for 2181 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 23: After refmac, R = 0.2157 (Rfree = 0.000) for 2161 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2189 (Rfree = 0.000) for 2155 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.2054 (Rfree = 0.000) for 2146 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.53 Search for helices and strands: 0 residues in 0 chains, 2260 seeds are put forward NCS extension: 0 residues added, 2260 seeds are put forward Round 1: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.327 Round 2: 146 peptides, 24 chains. Longest chain 17 peptides. Score 0.409 Round 3: 133 peptides, 20 chains. Longest chain 12 peptides. Score 0.429 Round 4: 131 peptides, 19 chains. Longest chain 16 peptides. Score 0.440 Round 5: 133 peptides, 21 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 4 Chains 19, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5066 restraints for refining 2229 atoms. 4637 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2244 (Rfree = 0.000) for 2229 atoms. Found 3 (12 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.2312 (Rfree = 0.000) for 2198 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2025 (Rfree = 0.000) for 2180 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.2048 (Rfree = 0.000) for 2167 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.1997 (Rfree = 0.000) for 2157 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.49 Search for helices and strands: 0 residues in 0 chains, 2271 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2289 seeds are put forward Round 1: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.272 Round 2: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.328 Round 3: 129 peptides, 20 chains. Longest chain 12 peptides. Score 0.412 Round 4: 124 peptides, 16 chains. Longest chain 19 peptides. Score 0.467 Round 5: 131 peptides, 20 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 4 Chains 16, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5152 restraints for refining 2228 atoms. 4736 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2349 (Rfree = 0.000) for 2228 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.2173 (Rfree = 0.000) for 2208 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.2320 (Rfree = 0.000) for 2203 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.2190 (Rfree = 0.000) for 2193 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.2312 (Rfree = 0.000) for 2185 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 2268 seeds are put forward NCS extension: 0 residues added, 2268 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.313 Round 2: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.299 Round 3: 116 peptides, 18 chains. Longest chain 13 peptides. Score 0.394 Round 4: 114 peptides, 19 chains. Longest chain 15 peptides. Score 0.365 Round 5: 121 peptides, 21 chains. Longest chain 9 peptides. Score 0.357 Taking the results from Round 3 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4939 restraints for refining 2174 atoms. 4565 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2001 (Rfree = 0.000) for 2174 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.2103 (Rfree = 0.000) for 2160 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.2249 (Rfree = 0.000) for 2152 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.2056 (Rfree = 0.000) for 2142 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.2159 (Rfree = 0.000) for 2140 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.53 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2245 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.247 Round 2: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.284 Round 3: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.298 Round 4: 104 peptides, 18 chains. Longest chain 11 peptides. Score 0.338 Round 5: 109 peptides, 20 chains. Longest chain 8 peptides. Score 0.320 Taking the results from Round 4 Chains 18, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4759 restraints for refining 2126 atoms. 4433 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2224 (Rfree = 0.000) for 2126 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2266 (Rfree = 0.000) for 2120 atoms. Found 9 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2123 (Rfree = 0.000) for 2106 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2027 (Rfree = 0.000) for 2094 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.2084 (Rfree = 0.000) for 2084 atoms. Found 3 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 2186 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 2190 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.236 Round 2: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.277 Round 3: 92 peptides, 15 chains. Longest chain 9 peptides. Score 0.345 Round 4: 86 peptides, 15 chains. Longest chain 8 peptides. Score 0.315 Round 5: 89 peptides, 15 chains. Longest chain 9 peptides. Score 0.330 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 77, 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 4580 restraints for refining 2032 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2325 (Rfree = 0.000) for 2032 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2315 (Rfree = 0.000) for 2020 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2065 (Rfree = 0.000) for 2006 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2150 (Rfree = 0.000) for 2001 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:00:23 GMT 2018 Job finished. TimeTaking 29.1 Used memory is bytes: 20528984