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 2gvk-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-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/2gvk-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-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/2gvk-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-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 272 and 0 Target number of residues in the AU: 272 Target solvent content: 0.6500 Checking the provided sequence file Detected sequence length: 317 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 317 Adjusted target solvent content: 0.59 Input MTZ file: 2gvk-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: 182 Cell parameters: 109.180 109.180 122.210 90.000 90.000 120.000 Input sequence file: 2gvk-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2536 target number of atoms Had to go as low as 0.90 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.072 3.800 Wilson plot Bfac: 77.35 4592 reflections ( 99.54 % complete ) and 0 restraints for refining 2799 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3447 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3232 (Rfree = 0.000) for 2799 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.22 Search for helices and strands: 0 residues in 0 chains, 2864 seeds are put forward Round 1: 163 peptides, 27 chains. Longest chain 14 peptides. Score 0.406 Round 2: 182 peptides, 24 chains. Longest chain 20 peptides. Score 0.521 Round 3: 194 peptides, 21 chains. Longest chain 25 peptides. Score 0.601 Round 4: 214 peptides, 21 chains. Longest chain 23 peptides. Score 0.656 Round 5: 223 peptides, 23 chains. Longest chain 20 peptides. Score 0.655 Taking the results from Round 4 Chains 21, Residues 193, Estimated correctness of the model 23.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 4882 restraints for refining 2294 atoms. 4095 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2529 (Rfree = 0.000) for 2294 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2395 (Rfree = 0.000) for 2239 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2304 (Rfree = 0.000) for 2217 atoms. Found 9 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2244 (Rfree = 0.000) for 2201 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2153 (Rfree = 0.000) for 2191 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.18 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward Round 1: 193 peptides, 27 chains. Longest chain 35 peptides. Score 0.513 Round 2: 221 peptides, 22 chains. Longest chain 24 peptides. Score 0.661 Round 3: 213 peptides, 23 chains. Longest chain 31 peptides. Score 0.628 Round 4: 216 peptides, 19 chains. Longest chain 26 peptides. Score 0.684 Round 5: 223 peptides, 24 chains. Longest chain 29 peptides. Score 0.643 Taking the results from Round 4 Chains 21, Residues 197, Estimated correctness of the model 34.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 4790 restraints for refining 2294 atoms. 3991 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2487 (Rfree = 0.000) for 2294 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 7: After refmac, R = 0.2333 (Rfree = 0.000) for 2265 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2217 (Rfree = 0.000) for 2255 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 9: After refmac, R = 0.2069 (Rfree = 0.000) for 2244 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2068 (Rfree = 0.000) for 2235 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.18 Search for helices and strands: 0 residues in 0 chains, 2338 seeds are put forward Round 1: 172 peptides, 25 chains. Longest chain 16 peptides. Score 0.471 Round 2: 202 peptides, 23 chains. Longest chain 25 peptides. Score 0.597 Round 3: 196 peptides, 24 chains. Longest chain 18 peptides. Score 0.566 Round 4: 216 peptides, 22 chains. Longest chain 25 peptides. Score 0.649 Round 5: 206 peptides, 22 chains. Longest chain 26 peptides. Score 0.622 Taking the results from Round 4 Chains 25, Residues 194, Estimated correctness of the model 20.4 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4592 reflections ( 99.54 % complete ) and 4786 restraints for refining 2293 atoms. 3959 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2444 (Rfree = 0.000) for 2293 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 12: After refmac, R = 0.2215 (Rfree = 0.000) for 2275 atoms. Found 10 (12 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.2102 (Rfree = 0.000) for 2262 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.2054 (Rfree = 0.000) for 2256 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2010 (Rfree = 0.000) for 2248 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.20 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward Round 1: 182 peptides, 25 chains. Longest chain 17 peptides. Score 0.506 Round 2: 206 peptides, 21 chains. Longest chain 25 peptides. Score 0.635 Round 3: 210 peptides, 25 chains. Longest chain 16 peptides. Score 0.594 Round 4: 211 peptides, 22 chains. Longest chain 33 peptides. Score 0.635 Round 5: 209 peptides, 26 chains. Longest chain 23 peptides. Score 0.578 Taking the results from Round 4 Chains 25, Residues 189, Estimated correctness of the model 14.5 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 4796 restraints for refining 2294 atoms. 3959 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2543 (Rfree = 0.000) for 2294 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2304 (Rfree = 0.000) for 2273 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.2169 (Rfree = 0.000) for 2264 atoms. Found 3 (12 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2114 (Rfree = 0.000) for 2252 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2107 (Rfree = 0.000) for 2243 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.21 Search for helices and strands: 0 residues in 0 chains, 2308 seeds are put forward Round 1: 177 peptides, 26 chains. Longest chain 12 peptides. Score 0.473 Round 2: 196 peptides, 24 chains. Longest chain 16 peptides. Score 0.566 Round 3: 197 peptides, 24 chains. Longest chain 16 peptides. Score 0.569 Round 4: 184 peptides, 21 chains. Longest chain 17 peptides. Score 0.571 Round 5: 185 peptides, 20 chains. Longest chain 19 peptides. Score 0.588 Taking the results from Round 5 Chains 20, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 5220 restraints for refining 2292 atoms. 4580 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2546 (Rfree = 0.000) for 2292 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 22: After refmac, R = 0.2390 (Rfree = 0.000) for 2283 atoms. Found 9 (12 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 2277 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2151 (Rfree = 0.000) for 2278 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2248 (Rfree = 0.000) for 2269 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.23 Search for helices and strands: 0 residues in 0 chains, 2343 seeds are put forward Round 1: 166 peptides, 28 chains. Longest chain 14 peptides. Score 0.400 Round 2: 183 peptides, 27 chains. Longest chain 14 peptides. Score 0.479 Round 3: 183 peptides, 24 chains. Longest chain 17 peptides. Score 0.524 Round 4: 192 peptides, 22 chains. Longest chain 23 peptides. Score 0.582 Round 5: 195 peptides, 23 chains. Longest chain 22 peptides. Score 0.577 Taking the results from Round 4 Chains 24, Residues 170, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 5030 restraints for refining 2293 atoms. 4335 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2418 (Rfree = 0.000) for 2293 atoms. Found 6 (12 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.2318 (Rfree = 0.000) for 2269 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2307 (Rfree = 0.000) for 2255 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.2230 (Rfree = 0.000) for 2247 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.2074 (Rfree = 0.000) for 2242 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.18 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 11 peptides. Score 0.388 Round 2: 190 peptides, 23 chains. Longest chain 22 peptides. Score 0.561 Round 3: 166 peptides, 25 chains. Longest chain 13 peptides. Score 0.450 Round 4: 165 peptides, 21 chains. Longest chain 17 peptides. Score 0.510 Round 5: 167 peptides, 22 chains. Longest chain 16 peptides. Score 0.501 Taking the results from Round 2 Chains 25, Residues 167, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 4970 restraints for refining 2293 atoms. 4286 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2266 (Rfree = 0.000) for 2293 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.2233 (Rfree = 0.000) for 2276 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2140 (Rfree = 0.000) for 2267 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2157 (Rfree = 0.000) for 2260 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2069 (Rfree = 0.000) for 2254 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.22 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward Round 1: 160 peptides, 29 chains. Longest chain 11 peptides. Score 0.360 Round 2: 182 peptides, 25 chains. Longest chain 16 peptides. Score 0.506 Round 3: 181 peptides, 26 chains. Longest chain 15 peptides. Score 0.487 Round 4: 185 peptides, 23 chains. Longest chain 17 peptides. Score 0.546 Round 5: 179 peptides, 22 chains. Longest chain 17 peptides. Score 0.541 Taking the results from Round 4 Chains 25, Residues 162, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4592 reflections ( 99.54 % complete ) and 5125 restraints for refining 2294 atoms. 4427 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2516 (Rfree = 0.000) for 2294 atoms. Found 8 (12 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2403 (Rfree = 0.000) for 2279 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2372 (Rfree = 0.000) for 2273 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2251 (Rfree = 0.000) for 2272 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2226 (Rfree = 0.000) for 2263 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.20 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward Round 1: 160 peptides, 28 chains. Longest chain 13 peptides. Score 0.377 Round 2: 158 peptides, 22 chains. Longest chain 17 peptides. Score 0.470 Round 3: 169 peptides, 24 chains. Longest chain 14 peptides. Score 0.477 Round 4: 169 peptides, 22 chains. Longest chain 13 peptides. Score 0.508 Round 5: 172 peptides, 19 chains. Longest chain 28 peptides. Score 0.563 Taking the results from Round 5 Chains 19, Residues 153, Estimated correctness of the model 0.0 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4592 reflections ( 99.54 % complete ) and 4931 restraints for refining 2294 atoms. 4219 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2531 (Rfree = 0.000) for 2294 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2524 (Rfree = 0.000) for 2281 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.2498 (Rfree = 0.000) for 2273 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2416 (Rfree = 0.000) for 2275 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2336 (Rfree = 0.000) for 2269 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.20 Search for helices and strands: 0 residues in 0 chains, 2347 seeds are put forward Round 1: 136 peptides, 24 chains. Longest chain 10 peptides. Score 0.350 Round 2: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.452 Round 3: 162 peptides, 23 chains. Longest chain 17 peptides. Score 0.468 Round 4: 161 peptides, 23 chains. Longest chain 15 peptides. Score 0.464 Round 5: 169 peptides, 24 chains. Longest chain 17 peptides. Score 0.477 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 145, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2gvk-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4592 reflections ( 99.54 % complete ) and 5276 restraints for refining 2293 atoms. 4680 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2504 (Rfree = 0.000) for 2293 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2463 (Rfree = 0.000) for 2273 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2340 (Rfree = 0.000) for 2258 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2298 (Rfree = 0.000) for 2246 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:23:42 GMT 2018 Job finished. TimeTaking 55.75