null Sun 23 Dec 22:23:10 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 2glz-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2glz-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2glz-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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/2glz-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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 22:23:19 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/2glz-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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 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-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: 19 Cell parameters: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-4.0-parrot-hancs.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 2712 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3502 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2915 (Rfree = 0.000) for 2712 atoms. Found 12 (12 requested) and removed 281 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 2460 seeds are put forward NCS extension: 0 residues added, 2460 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.242 Round 2: 132 peptides, 23 chains. Longest chain 15 peptides. Score 0.359 Round 3: 128 peptides, 22 chains. Longest chain 11 peptides. Score 0.361 Round 4: 144 peptides, 25 chains. Longest chain 11 peptides. Score 0.374 Round 5: 148 peptides, 25 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 5 Chains 25, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5172 restraints for refining 2208 atoms. 4705 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2916 (Rfree = 0.000) for 2208 atoms. Found 10 (10 requested) and removed 62 (5 requested) atoms. Cycle 2: After refmac, R = 0.2675 (Rfree = 0.000) for 2140 atoms. Found 10 (10 requested) and removed 30 (5 requested) atoms. Cycle 3: After refmac, R = 0.2326 (Rfree = 0.000) for 2104 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 4: After refmac, R = 0.2335 (Rfree = 0.000) for 2083 atoms. Found 1 (9 requested) and removed 19 (4 requested) atoms. Cycle 5: After refmac, R = 0.2169 (Rfree = 0.000) for 2061 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.26 Search for helices and strands: 0 residues in 0 chains, 2149 seeds are put forward NCS extension: 5 residues added (0 deleted due to clashes), 2154 seeds are put forward Round 1: 133 peptides, 24 chains. Longest chain 11 peptides. Score 0.345 Round 2: 151 peptides, 25 chains. Longest chain 11 peptides. Score 0.403 Round 3: 160 peptides, 22 chains. Longest chain 16 peptides. Score 0.489 Round 4: 160 peptides, 23 chains. Longest chain 24 peptides. Score 0.473 Round 5: 167 peptides, 24 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 3 Chains 22, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5022 restraints for refining 2210 atoms. 4492 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2431 (Rfree = 0.000) for 2210 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 7: After refmac, R = 0.2287 (Rfree = 0.000) for 2187 atoms. Found 4 (10 requested) and removed 19 (5 requested) atoms. Cycle 8: After refmac, R = 0.2087 (Rfree = 0.000) for 2168 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2146 (Rfree = 0.000) for 2162 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2032 (Rfree = 0.000) for 2153 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.26 Search for helices and strands: 0 residues in 0 chains, 2226 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2249 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 11 peptides. Score 0.352 Round 2: 157 peptides, 26 chains. Longest chain 12 peptides. Score 0.409 Round 3: 167 peptides, 27 chains. Longest chain 17 peptides. Score 0.432 Round 4: 166 peptides, 23 chains. Longest chain 21 peptides. Score 0.495 Round 5: 157 peptides, 23 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 4 Chains 23, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5012 restraints for refining 2211 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2457 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2222 (Rfree = 0.000) for 2200 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2161 (Rfree = 0.000) for 2188 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2155 (Rfree = 0.000) for 2187 atoms. Found 2 (10 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.2084 (Rfree = 0.000) for 2176 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 2279 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2303 seeds are put forward Round 1: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.371 Round 2: 164 peptides, 25 chains. Longest chain 15 peptides. Score 0.454 Round 3: 167 peptides, 25 chains. Longest chain 17 peptides. Score 0.466 Round 4: 163 peptides, 21 chains. Longest chain 21 peptides. Score 0.517 Round 5: 148 peptides, 20 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 4 Chains 21, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5048 restraints for refining 2210 atoms. 4501 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2546 (Rfree = 0.000) for 2210 atoms. Found 6 (10 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2359 (Rfree = 0.000) for 2191 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2335 (Rfree = 0.000) for 2186 atoms. Found 0 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2365 (Rfree = 0.000) for 2177 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2270 (Rfree = 0.000) for 2169 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 2264 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2283 seeds are put forward Round 1: 129 peptides, 22 chains. Longest chain 14 peptides. Score 0.365 Round 2: 139 peptides, 17 chains. Longest chain 19 peptides. Score 0.496 Round 3: 138 peptides, 19 chains. Longest chain 13 peptides. Score 0.457 Round 4: 147 peptides, 18 chains. Longest chain 25 peptides. Score 0.509 Round 5: 150 peptides, 21 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 4 Chains 18, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5109 restraints for refining 2210 atoms. 4611 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2572 (Rfree = 0.000) for 2210 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2377 (Rfree = 0.000) for 2207 atoms. Found 5 (10 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.2298 (Rfree = 0.000) for 2197 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2207 (Rfree = 0.000) for 2193 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2221 (Rfree = 0.000) for 2187 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.30 Search for helices and strands: 0 residues in 0 chains, 2269 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 2303 seeds are put forward Round 1: 124 peptides, 24 chains. Longest chain 9 peptides. Score 0.305 Round 2: 150 peptides, 26 chains. Longest chain 10 peptides. Score 0.381 Round 3: 162 peptides, 25 chains. Longest chain 16 peptides. Score 0.446 Round 4: 164 peptides, 27 chains. Longest chain 17 peptides. Score 0.420 Round 5: 165 peptides, 25 chains. Longest chain 17 peptides. Score 0.458 Taking the results from Round 5 Chains 25, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4940 restraints for refining 2211 atoms. 4405 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2449 (Rfree = 0.000) for 2211 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.2276 (Rfree = 0.000) for 2194 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2233 (Rfree = 0.000) for 2191 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2202 (Rfree = 0.000) for 2184 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2218 (Rfree = 0.000) for 2175 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2235 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2258 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 10 peptides. Score 0.311 Round 2: 148 peptides, 26 chains. Longest chain 13 peptides. Score 0.372 Round 3: 167 peptides, 24 chains. Longest chain 25 peptides. Score 0.482 Round 4: 166 peptides, 27 chains. Longest chain 16 peptides. Score 0.428 Round 5: 162 peptides, 24 chains. Longest chain 13 peptides. Score 0.463 Taking the results from Round 3 Chains 24, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4940 restraints for refining 2211 atoms. 4392 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2495 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.2457 (Rfree = 0.000) for 2203 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2267 (Rfree = 0.000) for 2192 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2194 (Rfree = 0.000) for 2180 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.2236 (Rfree = 0.000) for 2172 atoms. Found 6 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2236 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 2267 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 12 peptides. Score 0.291 Round 2: 150 peptides, 27 chains. Longest chain 10 peptides. Score 0.363 Round 3: 158 peptides, 28 chains. Longest chain 12 peptides. Score 0.378 Round 4: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.403 Round 5: 164 peptides, 29 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 4 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5041 restraints for refining 2211 atoms. 4562 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2486 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2343 (Rfree = 0.000) for 2202 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2152 (Rfree = 0.000) for 2186 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.2108 (Rfree = 0.000) for 2174 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1957 (Rfree = 0.000) for 2166 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.29 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2237 seeds are put forward Round 1: 126 peptides, 28 chains. Longest chain 7 peptides. Score 0.236 Round 2: 139 peptides, 25 chains. Longest chain 12 peptides. Score 0.352 Round 3: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.358 Round 4: 143 peptides, 23 chains. Longest chain 20 peptides. Score 0.406 Round 5: 139 peptides, 22 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5178 restraints for refining 2210 atoms. 4732 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2292 (Rfree = 0.000) for 2210 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2202 (Rfree = 0.000) for 2206 atoms. Found 7 (10 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2057 (Rfree = 0.000) for 2198 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2107 (Rfree = 0.000) for 2190 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2016 (Rfree = 0.000) for 2184 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.27 Search for helices and strands: 0 residues in 0 chains, 2256 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2273 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.230 Round 2: 134 peptides, 24 chains. Longest chain 9 peptides. Score 0.349 Round 3: 131 peptides, 23 chains. Longest chain 12 peptides. Score 0.355 Round 4: 134 peptides, 23 chains. Longest chain 15 peptides. Score 0.368 Round 5: 137 peptides, 24 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 111, 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 5258 restraints for refining 2211 atoms. 4837 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2377 (Rfree = 0.000) for 2211 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2363 (Rfree = 0.000) for 2199 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2207 (Rfree = 0.000) for 2192 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2221 (Rfree = 0.000) for 2183 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:08 GMT 2018 Job finished. TimeTaking 42.97 Used memory is bytes: 14630832