Sun 23 Dec 22:22:56 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 1vpb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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/1vpb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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 22:23:06 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/1vpb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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 386 and 0 Target number of residues in the AU: 386 Target solvent content: 0.6558 Checking the provided sequence file Detected sequence length: 451 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 451 Adjusted target solvent content: 0.60 Input MTZ file: 1vpb-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: 20 Cell parameters: 74.004 155.044 105.800 90.000 90.000 90.000 Input sequence file: 1vpb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3608 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 Loops will be built when appropriate and at the last cycle Resolution range: 77.522 4.000 Wilson plot Bfac: 81.68 5351 reflections ( 98.98 % complete ) and 0 restraints for refining 3993 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3183 (Rfree = 0.000) for 3993 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.22 Search for helices and strands: 0 residues in 0 chains, 4088 seeds are put forward Round 1: 194 peptides, 36 chains. Longest chain 11 peptides. Score 0.326 Round 2: 239 peptides, 34 chains. Longest chain 17 peptides. Score 0.471 Round 3: 252 peptides, 34 chains. Longest chain 22 peptides. Score 0.503 Round 4: 260 peptides, 31 chains. Longest chain 27 peptides. Score 0.552 Round 5: 267 peptides, 32 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 5 Chains 36, Residues 235, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 7131 restraints for refining 3258 atoms. 6118 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2482 (Rfree = 0.000) for 3258 atoms. Found 8 (15 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2228 (Rfree = 0.000) for 3190 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. Cycle 3: After refmac, R = 0.2140 (Rfree = 0.000) for 3160 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2110 (Rfree = 0.000) for 3141 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.2068 (Rfree = 0.000) for 3133 atoms. Found 1 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 3241 seeds are put forward Round 1: 233 peptides, 40 chains. Longest chain 11 peptides. Score 0.387 Round 2: 264 peptides, 34 chains. Longest chain 19 peptides. Score 0.530 Round 3: 277 peptides, 37 chains. Longest chain 15 peptides. Score 0.529 Round 4: 271 peptides, 31 chains. Longest chain 20 peptides. Score 0.576 Round 5: 276 peptides, 30 chains. Longest chain 38 peptides. Score 0.596 Taking the results from Round 5 Chains 30, Residues 246, Estimated correctness of the model 0.0 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 6935 restraints for refining 3258 atoms. 5775 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2362 (Rfree = 0.000) for 3258 atoms. Found 14 (15 requested) and removed 24 (7 requested) atoms. Cycle 7: After refmac, R = 0.2269 (Rfree = 0.000) for 3202 atoms. Found 14 (15 requested) and removed 17 (7 requested) atoms. Cycle 8: After refmac, R = 0.2222 (Rfree = 0.000) for 3169 atoms. Found 6 (15 requested) and removed 24 (7 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 3142 atoms. Found 7 (14 requested) and removed 20 (7 requested) atoms. Cycle 10: After refmac, R = 0.2048 (Rfree = 0.000) for 3118 atoms. Found 1 (14 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 3184 seeds are put forward Round 1: 226 peptides, 36 chains. Longest chain 14 peptides. Score 0.415 Round 2: 235 peptides, 29 chains. Longest chain 19 peptides. Score 0.516 Round 3: 260 peptides, 33 chains. Longest chain 17 peptides. Score 0.532 Round 4: 273 peptides, 35 chains. Longest chain 22 peptides. Score 0.540 Round 5: 269 peptides, 31 chains. Longest chain 19 peptides. Score 0.572 Taking the results from Round 5 Chains 36, Residues 238, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 6891 restraints for refining 3258 atoms. 5849 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2244 (Rfree = 0.000) for 3258 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 12: After refmac, R = 0.2046 (Rfree = 0.000) for 3223 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 13: After refmac, R = 0.2012 (Rfree = 0.000) for 3208 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.1978 (Rfree = 0.000) for 3197 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.1968 (Rfree = 0.000) for 3187 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.18 Search for helices and strands: 0 residues in 0 chains, 3296 seeds are put forward Round 1: 220 peptides, 35 chains. Longest chain 15 peptides. Score 0.411 Round 2: 254 peptides, 34 chains. Longest chain 18 peptides. Score 0.507 Round 3: 241 peptides, 32 chains. Longest chain 16 peptides. Score 0.498 Round 4: 248 peptides, 28 chains. Longest chain 25 peptides. Score 0.556 Round 5: 261 peptides, 28 chains. Longest chain 25 peptides. Score 0.584 Taking the results from Round 5 Chains 28, Residues 233, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 6967 restraints for refining 3258 atoms. 5925 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2210 (Rfree = 0.000) for 3258 atoms. Found 10 (15 requested) and removed 17 (7 requested) atoms. Cycle 17: After refmac, R = 0.2034 (Rfree = 0.000) for 3218 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.1965 (Rfree = 0.000) for 3200 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.1937 (Rfree = 0.000) for 3185 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 3176 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 3262 seeds are put forward Round 1: 225 peptides, 40 chains. Longest chain 12 peptides. Score 0.366 Round 2: 246 peptides, 33 chains. Longest chain 16 peptides. Score 0.499 Round 3: 257 peptides, 36 chains. Longest chain 19 peptides. Score 0.493 Round 4: 249 peptides, 35 chains. Longest chain 31 peptides. Score 0.485 Round 5: 252 peptides, 33 chains. Longest chain 26 peptides. Score 0.513 Taking the results from Round 5 Chains 34, Residues 219, Estimated correctness of the model 0.0 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 7260 restraints for refining 3258 atoms. 6318 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2437 (Rfree = 0.000) for 3258 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.2271 (Rfree = 0.000) for 3228 atoms. Found 9 (15 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2233 (Rfree = 0.000) for 3197 atoms. Found 9 (15 requested) and removed 15 (7 requested) atoms. Cycle 24: After refmac, R = 0.2130 (Rfree = 0.000) for 3172 atoms. Found 11 (15 requested) and removed 12 (7 requested) atoms. Cycle 25: After refmac, R = 0.1768 (Rfree = 0.000) for 3155 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.24 Search for helices and strands: 0 residues in 0 chains, 3246 seeds are put forward Round 1: 213 peptides, 41 chains. Longest chain 9 peptides. Score 0.319 Round 2: 244 peptides, 34 chains. Longest chain 21 peptides. Score 0.484 Round 3: 245 peptides, 34 chains. Longest chain 17 peptides. Score 0.486 Round 4: 233 peptides, 33 chains. Longest chain 17 peptides. Score 0.468 Round 5: 227 peptides, 30 chains. Longest chain 16 peptides. Score 0.486 Taking the results from Round 5 Chains 30, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 7650 restraints for refining 3258 atoms. 6892 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2354 (Rfree = 0.000) for 3258 atoms. Found 14 (15 requested) and removed 18 (7 requested) atoms. Cycle 27: After refmac, R = 0.2327 (Rfree = 0.000) for 3209 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2254 (Rfree = 0.000) for 3189 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.2402 (Rfree = 0.000) for 3176 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.2195 (Rfree = 0.000) for 3155 atoms. Found 7 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.21 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 8 peptides. Score 0.248 Round 2: 204 peptides, 33 chains. Longest chain 14 peptides. Score 0.392 Round 3: 217 peptides, 35 chains. Longest chain 16 peptides. Score 0.403 Round 4: 219 peptides, 35 chains. Longest chain 13 peptides. Score 0.409 Round 5: 226 peptides, 32 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 5 Chains 33, Residues 194, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 7205 restraints for refining 3258 atoms. 6372 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2208 (Rfree = 0.000) for 3258 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2077 (Rfree = 0.000) for 3214 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 33: After refmac, R = 0.1972 (Rfree = 0.000) for 3189 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.1950 (Rfree = 0.000) for 3174 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 3162 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.23 Search for helices and strands: 0 residues in 0 chains, 3272 seeds are put forward Round 1: 180 peptides, 37 chains. Longest chain 10 peptides. Score 0.272 Round 2: 203 peptides, 36 chains. Longest chain 11 peptides. Score 0.352 Round 3: 203 peptides, 35 chains. Longest chain 14 peptides. Score 0.365 Round 4: 217 peptides, 37 chains. Longest chain 12 peptides. Score 0.379 Round 5: 198 peptides, 34 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 4 Chains 37, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 7544 restraints for refining 3258 atoms. 6861 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2284 (Rfree = 0.000) for 3258 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.2324 (Rfree = 0.000) for 3232 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.2371 (Rfree = 0.000) for 3204 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 3184 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.2337 (Rfree = 0.000) for 3163 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 3294 seeds are put forward Round 1: 165 peptides, 36 chains. Longest chain 9 peptides. Score 0.237 Round 2: 177 peptides, 33 chains. Longest chain 10 peptides. Score 0.314 Round 3: 182 peptides, 32 chains. Longest chain 11 peptides. Score 0.342 Round 4: 185 peptides, 33 chains. Longest chain 16 peptides. Score 0.338 Round 5: 196 peptides, 33 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 5 Chains 33, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5351 reflections ( 98.98 % complete ) and 7643 restraints for refining 3258 atoms. 7024 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2298 (Rfree = 0.000) for 3258 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.2377 (Rfree = 0.000) for 3225 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 43: After refmac, R = 0.2194 (Rfree = 0.000) for 3197 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.2016 (Rfree = 0.000) for 3191 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.2210 (Rfree = 0.000) for 3187 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 3296 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 8 peptides. Score 0.256 Round 2: 173 peptides, 31 chains. Longest chain 13 peptides. Score 0.328 Round 3: 178 peptides, 29 chains. Longest chain 13 peptides. Score 0.369 Round 4: 179 peptides, 29 chains. Longest chain 13 peptides. Score 0.372 Round 5: 193 peptides, 31 chains. Longest chain 26 peptides. Score 0.386 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 162, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vpb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5351 reflections ( 98.98 % complete ) and 7381 restraints for refining 3258 atoms. 6729 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2236 (Rfree = 0.000) for 3258 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2306 (Rfree = 0.000) for 3200 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2317 (Rfree = 0.000) for 3167 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2220 (Rfree = 0.000) for 3147 atoms. TimeTaking 56.52