null Sun 23 Dec 22:23:05 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.6-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 22:23:15 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-3.6-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 282 and 0 Target number of residues in the AU: 282 Target solvent content: 0.6371 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 69.85 5367 reflections ( 99.59 % complete ) and 0 restraints for refining 2832 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3315 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3267 (Rfree = 0.000) for 2832 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.04 Search for helices and strands: 0 residues in 0 chains, 2887 seeds are put forward Round 1: 172 peptides, 30 chains. Longest chain 13 peptides. Score 0.390 Round 2: 209 peptides, 26 chains. Longest chain 26 peptides. Score 0.578 Round 3: 209 peptides, 27 chains. Longest chain 18 peptides. Score 0.564 Round 4: 216 peptides, 24 chains. Longest chain 18 peptides. Score 0.624 Round 5: 208 peptides, 23 chains. Longest chain 29 peptides. Score 0.614 Taking the results from Round 4 Chains 24, Residues 192, Estimated correctness of the model 23.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 5001 restraints for refining 2299 atoms. 4257 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2469 (Rfree = 0.000) for 2299 atoms. Found 12 (14 requested) and removed 12 (7 requested) atoms. Cycle 2: After refmac, R = 0.2327 (Rfree = 0.000) for 2268 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2195 (Rfree = 0.000) for 2252 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 4: After refmac, R = 0.2172 (Rfree = 0.000) for 2239 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.2072 (Rfree = 0.000) for 2233 atoms. Found 6 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.02 Search for helices and strands: 0 residues in 0 chains, 2326 seeds are put forward Round 1: 169 peptides, 26 chains. Longest chain 17 peptides. Score 0.445 Round 2: 182 peptides, 22 chains. Longest chain 20 peptides. Score 0.551 Round 3: 200 peptides, 25 chains. Longest chain 22 peptides. Score 0.564 Round 4: 189 peptides, 25 chains. Longest chain 16 peptides. Score 0.529 Round 5: 216 peptides, 24 chains. Longest chain 25 peptides. Score 0.624 Taking the results from Round 5 Chains 25, Residues 192, Estimated correctness of the model 23.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4858 restraints for refining 2299 atoms. 4084 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2350 (Rfree = 0.000) for 2299 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 7: After refmac, R = 0.2166 (Rfree = 0.000) for 2280 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.2159 (Rfree = 0.000) for 2267 atoms. Found 12 (14 requested) and removed 14 (7 requested) atoms. Cycle 9: After refmac, R = 0.2051 (Rfree = 0.000) for 2260 atoms. Found 4 (14 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2074 (Rfree = 0.000) for 2251 atoms. Found 11 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.04 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward Round 1: 189 peptides, 28 chains. Longest chain 14 peptides. Score 0.484 Round 2: 211 peptides, 26 chains. Longest chain 19 peptides. Score 0.584 Round 3: 215 peptides, 24 chains. Longest chain 41 peptides. Score 0.621 Round 4: 208 peptides, 24 chains. Longest chain 25 peptides. Score 0.601 Round 5: 205 peptides, 22 chains. Longest chain 21 peptides. Score 0.619 Taking the results from Round 3 Chains 26, Residues 191, Estimated correctness of the model 22.7 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4653 restraints for refining 2299 atoms. 3851 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 2299 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2419 (Rfree = 0.000) for 2288 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.2334 (Rfree = 0.000) for 2282 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.2231 (Rfree = 0.000) for 2277 atoms. Found 9 (14 requested) and removed 17 (7 requested) atoms. Cycle 15: After refmac, R = 0.2204 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.01 Search for helices and strands: 0 residues in 0 chains, 2363 seeds are put forward Round 1: 190 peptides, 27 chains. Longest chain 17 peptides. Score 0.503 Round 2: 203 peptides, 25 chains. Longest chain 23 peptides. Score 0.573 Round 3: 198 peptides, 19 chains. Longest chain 41 peptides. Score 0.639 Round 4: 191 peptides, 20 chains. Longest chain 25 peptides. Score 0.606 Round 5: 185 peptides, 22 chains. Longest chain 19 peptides. Score 0.560 Taking the results from Round 3 Chains 21, Residues 179, Estimated correctness of the model 29.3 % 4 chains (62 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4338 restraints for refining 2299 atoms. 3403 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2561 (Rfree = 0.000) for 2299 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 17: After refmac, R = 0.2495 (Rfree = 0.000) for 2261 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 18: After refmac, R = 0.2345 (Rfree = 0.000) for 2247 atoms. Found 11 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.2659 (Rfree = 0.000) for 2240 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 2228 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.01 Search for helices and strands: 0 residues in 0 chains, 2321 seeds are put forward Round 1: 173 peptides, 24 chains. Longest chain 14 peptides. Score 0.491 Round 2: 195 peptides, 25 chains. Longest chain 22 peptides. Score 0.549 Round 3: 199 peptides, 22 chains. Longest chain 16 peptides. Score 0.602 Round 4: 200 peptides, 26 chains. Longest chain 19 peptides. Score 0.550 Round 5: 194 peptides, 25 chains. Longest chain 16 peptides. Score 0.545 Taking the results from Round 3 Chains 25, Residues 177, Estimated correctness of the model 15.4 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4772 restraints for refining 2299 atoms. 4010 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2487 (Rfree = 0.000) for 2299 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 22: After refmac, R = 0.2330 (Rfree = 0.000) for 2290 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 23: After refmac, R = 0.2192 (Rfree = 0.000) for 2278 atoms. Found 13 (14 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2211 (Rfree = 0.000) for 2278 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.2120 (Rfree = 0.000) for 2265 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.05 Search for helices and strands: 0 residues in 0 chains, 2340 seeds are put forward Round 1: 179 peptides, 26 chains. Longest chain 17 peptides. Score 0.480 Round 2: 197 peptides, 27 chains. Longest chain 20 peptides. Score 0.526 Round 3: 202 peptides, 27 chains. Longest chain 18 peptides. Score 0.542 Round 4: 204 peptides, 24 chains. Longest chain 20 peptides. Score 0.590 Round 5: 209 peptides, 24 chains. Longest chain 21 peptides. Score 0.604 Taking the results from Round 5 Chains 24, Residues 185, Estimated correctness of the model 16.2 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4881 restraints for refining 2299 atoms. 4145 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2413 (Rfree = 0.000) for 2299 atoms. Found 12 (14 requested) and removed 15 (7 requested) atoms. Cycle 27: After refmac, R = 0.2184 (Rfree = 0.000) for 2284 atoms. Found 12 (14 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2236 (Rfree = 0.000) for 2284 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.2074 (Rfree = 0.000) for 2278 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2144 (Rfree = 0.000) for 2270 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.00 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward Round 1: 174 peptides, 25 chains. Longest chain 16 peptides. Score 0.478 Round 2: 199 peptides, 26 chains. Longest chain 18 peptides. Score 0.547 Round 3: 198 peptides, 24 chains. Longest chain 21 peptides. Score 0.572 Round 4: 216 peptides, 25 chains. Longest chain 18 peptides. Score 0.611 Round 5: 197 peptides, 23 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 4 Chains 25, Residues 191, Estimated correctness of the model 18.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4792 restraints for refining 2299 atoms. 3994 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2297 (Rfree = 0.000) for 2299 atoms. Found 13 (14 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2145 (Rfree = 0.000) for 2295 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.2134 (Rfree = 0.000) for 2295 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.2058 (Rfree = 0.000) for 2289 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.2010 (Rfree = 0.000) for 2284 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.04 Search for helices and strands: 0 residues in 0 chains, 2368 seeds are put forward Round 1: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.425 Round 2: 183 peptides, 23 chains. Longest chain 17 peptides. Score 0.539 Round 3: 197 peptides, 24 chains. Longest chain 23 peptides. Score 0.569 Round 4: 182 peptides, 23 chains. Longest chain 16 peptides. Score 0.536 Round 5: 195 peptides, 28 chains. Longest chain 16 peptides. Score 0.505 Taking the results from Round 3 Chains 25, Residues 173, Estimated correctness of the model 2.2 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 4818 restraints for refining 2299 atoms. 4075 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2408 (Rfree = 0.000) for 2299 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. Cycle 37: After refmac, R = 0.2297 (Rfree = 0.000) for 2280 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 2275 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.2276 (Rfree = 0.000) for 2271 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.2138 (Rfree = 0.000) for 2270 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.03 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward Round 1: 172 peptides, 25 chains. Longest chain 22 peptides. Score 0.471 Round 2: 196 peptides, 26 chains. Longest chain 17 peptides. Score 0.537 Round 3: 199 peptides, 22 chains. Longest chain 24 peptides. Score 0.602 Round 4: 192 peptides, 24 chains. Longest chain 23 peptides. Score 0.553 Round 5: 188 peptides, 21 chains. Longest chain 24 peptides. Score 0.583 Taking the results from Round 3 Chains 22, Residues 177, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.59 % complete ) and 5025 restraints for refining 2298 atoms. 4339 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2412 (Rfree = 0.000) for 2298 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.2300 (Rfree = 0.000) for 2298 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.2257 (Rfree = 0.000) for 2294 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 44: After refmac, R = 0.2257 (Rfree = 0.000) for 2289 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.2173 (Rfree = 0.000) for 2290 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.00 Search for helices and strands: 0 residues in 0 chains, 2344 seeds are put forward Round 1: 167 peptides, 28 chains. Longest chain 12 peptides. Score 0.404 Round 2: 179 peptides, 20 chains. Longest chain 17 peptides. Score 0.570 Round 3: 192 peptides, 24 chains. Longest chain 22 peptides. Score 0.553 Round 4: 187 peptides, 22 chains. Longest chain 29 peptides. Score 0.566 Round 5: 182 peptides, 21 chains. Longest chain 21 peptides. Score 0.565 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 159, Estimated correctness of the model 2.6 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gvk-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5367 reflections ( 99.59 % complete ) and 5113 restraints for refining 2299 atoms. 4497 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2389 (Rfree = 0.000) for 2299 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2231 (Rfree = 0.000) for 2286 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2200 (Rfree = 0.000) for 2279 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2117 (Rfree = 0.000) for 2268 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:18 GMT 2018 Job finished. TimeTaking 54.21 Used memory is bytes: 16331352