Mon 24 Dec 07:30:24 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 2glz-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2glz-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2glz-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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/2glz-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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 07:30:28 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/2glz-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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 263 and 0 Target number of residues in the AU: 263 Target solvent content: 0.6409 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.58 Input MTZ file: 2glz-4.0-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: 19 Cell parameters: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.85 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: 29.894 4.000 Wilson plot Bfac: 72.38 3639 reflections ( 99.62 % complete ) and 0 restraints for refining 2720 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3630 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2677 (Rfree = 0.000) for 2720 atoms. Found 11 (12 requested) and removed 30 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.24 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: 137 peptides, 29 chains. Longest chain 9 peptides. Score 0.268 Round 2: 173 peptides, 32 chains. Longest chain 9 peptides. Score 0.369 Round 3: 181 peptides, 32 chains. Longest chain 10 peptides. Score 0.402 Round 4: 188 peptides, 31 chains. Longest chain 11 peptides. Score 0.446 Round 5: 176 peptides, 28 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 5 Chains 28, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5129 restraints for refining 2211 atoms. 4565 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2721 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. Cycle 2: After refmac, R = 0.2456 (Rfree = 0.000) for 2166 atoms. Found 6 (10 requested) and removed 21 (5 requested) atoms. Cycle 3: After refmac, R = 0.2431 (Rfree = 0.000) for 2140 atoms. Found 7 (10 requested) and removed 17 (5 requested) atoms. Cycle 4: After refmac, R = 0.2343 (Rfree = 0.000) for 2121 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2158 (Rfree = 0.000) for 2106 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.30 Search for helices and strands: 0 residues in 0 chains, 2206 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2218 seeds are put forward Round 1: 176 peptides, 35 chains. Longest chain 9 peptides. Score 0.329 Round 2: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.426 Round 3: 180 peptides, 25 chains. Longest chain 18 peptides. Score 0.513 Round 4: 168 peptides, 23 chains. Longest chain 21 peptides. Score 0.502 Round 5: 171 peptides, 23 chains. Longest chain 22 peptides. Score 0.513 Taking the results from Round 5 Chains 23, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5023 restraints for refining 2211 atoms. 4454 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2477 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.2318 (Rfree = 0.000) for 2199 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 8: After refmac, R = 0.2442 (Rfree = 0.000) for 2191 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.2271 (Rfree = 0.000) for 2182 atoms. Found 4 (10 requested) and removed 12 (5 requested) atoms. Cycle 10: After refmac, R = 0.2350 (Rfree = 0.000) for 2168 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.28 Search for helices and strands: 0 residues in 0 chains, 2277 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 2311 seeds are put forward Round 1: 146 peptides, 24 chains. Longest chain 16 peptides. Score 0.400 Round 2: 157 peptides, 23 chains. Longest chain 15 peptides. Score 0.461 Round 3: 166 peptides, 25 chains. Longest chain 11 peptides. Score 0.462 Round 4: 172 peptides, 27 chains. Longest chain 13 peptides. Score 0.451 Round 5: 173 peptides, 27 chains. Longest chain 12 peptides. Score 0.455 Taking the results from Round 3 Chains 25, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4932 restraints for refining 2210 atoms. 4393 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2464 (Rfree = 0.000) for 2210 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 12: After refmac, R = 0.2586 (Rfree = 0.000) for 2200 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2342 (Rfree = 0.000) for 2197 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.2334 (Rfree = 0.000) for 2185 atoms. Found 1 (10 requested) and removed 13 (5 requested) atoms. Cycle 15: After refmac, R = 0.2377 (Rfree = 0.000) for 2171 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 2263 seeds are put forward Round 1: 144 peptides, 26 chains. Longest chain 13 peptides. Score 0.355 Round 2: 153 peptides, 23 chains. Longest chain 14 peptides. Score 0.446 Round 3: 161 peptides, 25 chains. Longest chain 14 peptides. Score 0.443 Round 4: 168 peptides, 25 chains. Longest chain 18 peptides. Score 0.469 Round 5: 168 peptides, 25 chains. Longest chain 13 peptides. Score 0.469 Taking the results from Round 5 Chains 25, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5085 restraints for refining 2210 atoms. 4538 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2550 (Rfree = 0.000) for 2210 atoms. Found 5 (10 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.2358 (Rfree = 0.000) for 2196 atoms. Found 2 (10 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2330 (Rfree = 0.000) for 2182 atoms. Found 3 (10 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2319 (Rfree = 0.000) for 2174 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 20: After refmac, R = 0.2371 (Rfree = 0.000) for 2167 atoms. Found 1 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.29 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 2257 seeds are put forward Round 1: 131 peptides, 25 chains. Longest chain 10 peptides. Score 0.317 Round 2: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.463 Round 3: 149 peptides, 22 chains. Longest chain 20 peptides. Score 0.448 Round 4: 161 peptides, 23 chains. Longest chain 18 peptides. Score 0.476 Round 5: 178 peptides, 22 chains. Longest chain 23 peptides. Score 0.553 Taking the results from Round 5 Chains 22, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4974 restraints for refining 2209 atoms. 4372 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2606 (Rfree = 0.000) for 2209 atoms. Found 8 (10 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.2375 (Rfree = 0.000) for 2194 atoms. Found 1 (10 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2295 (Rfree = 0.000) for 2181 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2241 (Rfree = 0.000) for 2172 atoms. Found 0 (10 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.2221 (Rfree = 0.000) for 2159 atoms. Found 2 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 2214 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 2244 seeds are put forward Round 1: 148 peptides, 30 chains. Longest chain 8 peptides. Score 0.299 Round 2: 165 peptides, 28 chains. Longest chain 10 peptides. Score 0.407 Round 3: 168 peptides, 24 chains. Longest chain 13 peptides. Score 0.486 Round 4: 176 peptides, 29 chains. Longest chain 13 peptides. Score 0.433 Round 5: 182 peptides, 26 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 5 Chains 26, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4860 restraints for refining 2211 atoms. 4262 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2669 (Rfree = 0.000) for 2211 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.2430 (Rfree = 0.000) for 2199 atoms. Found 1 (10 requested) and removed 16 (5 requested) atoms. Cycle 28: After refmac, R = 0.2401 (Rfree = 0.000) for 2181 atoms. Found 3 (10 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.2362 (Rfree = 0.000) for 2171 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2320 (Rfree = 0.000) for 2165 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.28 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 2289 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 8 peptides. Score 0.295 Round 2: 163 peptides, 28 chains. Longest chain 9 peptides. Score 0.399 Round 3: 153 peptides, 25 chains. Longest chain 10 peptides. Score 0.411 Round 4: 156 peptides, 29 chains. Longest chain 9 peptides. Score 0.352 Round 5: 152 peptides, 27 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 3 Chains 25, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5020 restraints for refining 2211 atoms. 4533 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2641 (Rfree = 0.000) for 2211 atoms. Found 6 (10 requested) and removed 17 (5 requested) atoms. Cycle 32: After refmac, R = 0.2417 (Rfree = 0.000) for 2199 atoms. Found 2 (10 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2401 (Rfree = 0.000) for 2189 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2377 (Rfree = 0.000) for 2181 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2393 (Rfree = 0.000) for 2174 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 2260 seeds are put forward NCS extension: 8 residues added (4 deleted due to clashes), 2268 seeds are put forward Round 1: 130 peptides, 27 chains. Longest chain 9 peptides. Score 0.274 Round 2: 148 peptides, 25 chains. Longest chain 10 peptides. Score 0.390 Round 3: 161 peptides, 25 chains. Longest chain 13 peptides. Score 0.443 Round 4: 147 peptides, 24 chains. Longest chain 9 peptides. Score 0.404 Round 5: 150 peptides, 23 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 3 Chains 26, Residues 136, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4962 restraints for refining 2211 atoms. 4398 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2565 (Rfree = 0.000) for 2211 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2377 (Rfree = 0.000) for 2199 atoms. Found 1 (10 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.2309 (Rfree = 0.000) for 2189 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2334 (Rfree = 0.000) for 2183 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2274 (Rfree = 0.000) for 2180 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.35 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2248 seeds are put forward Round 1: 119 peptides, 27 chains. Longest chain 7 peptides. Score 0.222 Round 2: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.365 Round 3: 144 peptides, 24 chains. Longest chain 14 peptides. Score 0.392 Round 4: 146 peptides, 23 chains. Longest chain 14 peptides. Score 0.418 Round 5: 135 peptides, 21 chains. Longest chain 11 peptides. Score 0.409 Taking the results from Round 4 Chains 23, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5167 restraints for refining 2211 atoms. 4698 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2520 (Rfree = 0.000) for 2211 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.2325 (Rfree = 0.000) for 2208 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2231 (Rfree = 0.000) for 2207 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2228 (Rfree = 0.000) for 2202 atoms. Found 0 (10 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2249 (Rfree = 0.000) for 2193 atoms. Found 4 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2243 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2263 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 9 peptides. Score 0.276 Round 2: 137 peptides, 25 chains. Longest chain 12 peptides. Score 0.344 Round 3: 128 peptides, 24 chains. Longest chain 7 peptides. Score 0.323 Round 4: 134 peptides, 24 chains. Longest chain 9 peptides. Score 0.349 Round 5: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 110, 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 2glz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3639 reflections ( 99.62 % complete ) and 5151 restraints for refining 2210 atoms. 4735 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2442 (Rfree = 0.000) for 2210 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2376 (Rfree = 0.000) for 2196 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2343 (Rfree = 0.000) for 2186 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2345 (Rfree = 0.000) for 2180 atoms. TimeTaking 26.82