null Sun 23 Dec 22:22:49 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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/1vpb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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 ============================================================ Sun 23 Dec 22:22:59 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-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 398 and 0 Target number of residues in the AU: 398 Target solvent content: 0.6451 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-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: 20 Cell parameters: 74.004 155.044 105.800 90.000 90.000 90.000 Input sequence file: 1vpb-3.8-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 3.800 Wilson plot Bfac: 75.11 6212 reflections ( 99.04 % complete ) and 0 restraints for refining 4002 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3118 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3032 (Rfree = 0.000) for 4002 atoms. Found 22 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.08 Search for helices and strands: 0 residues in 0 chains, 4071 seeds are put forward Round 1: 219 peptides, 39 chains. Longest chain 12 peptides. Score 0.361 Round 2: 292 peptides, 40 chains. Longest chain 20 peptides. Score 0.533 Round 3: 286 peptides, 35 chains. Longest chain 20 peptides. Score 0.569 Round 4: 294 peptides, 34 chains. Longest chain 21 peptides. Score 0.595 Round 5: 311 peptides, 35 chains. Longest chain 18 peptides. Score 0.619 Taking the results from Round 5 Chains 38, Residues 276, Estimated correctness of the model 7.5 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 6589 restraints for refining 3263 atoms. 5344 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2791 (Rfree = 0.000) for 3263 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2511 (Rfree = 0.000) for 3182 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.2514 (Rfree = 0.000) for 3136 atoms. Found 9 (17 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.2248 (Rfree = 0.000) for 3084 atoms. Found 8 (17 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.2395 (Rfree = 0.000) for 3054 atoms. Found 7 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.06 Search for helices and strands: 0 residues in 0 chains, 3157 seeds are put forward Round 1: 263 peptides, 37 chains. Longest chain 18 peptides. Score 0.497 Round 2: 304 peptides, 37 chains. Longest chain 24 peptides. Score 0.587 Round 3: 307 peptides, 37 chains. Longest chain 20 peptides. Score 0.593 Round 4: 309 peptides, 35 chains. Longest chain 31 peptides. Score 0.615 Round 5: 285 peptides, 33 chains. Longest chain 18 peptides. Score 0.586 Taking the results from Round 4 Chains 36, Residues 274, Estimated correctness of the model 5.7 % 4 chains (63 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 6551 restraints for refining 3264 atoms. 5245 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2498 (Rfree = 0.000) for 3264 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 7: After refmac, R = 0.2304 (Rfree = 0.000) for 3228 atoms. Found 5 (17 requested) and removed 20 (8 requested) atoms. Cycle 8: After refmac, R = 0.2192 (Rfree = 0.000) for 3205 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2094 (Rfree = 0.000) for 3186 atoms. Found 3 (17 requested) and removed 17 (8 requested) atoms. Cycle 10: After refmac, R = 0.2074 (Rfree = 0.000) for 3165 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 3271 seeds are put forward Round 1: 267 peptides, 40 chains. Longest chain 15 peptides. Score 0.475 Round 2: 264 peptides, 29 chains. Longest chain 19 peptides. Score 0.581 Round 3: 283 peptides, 36 chains. Longest chain 23 peptides. Score 0.552 Round 4: 267 peptides, 31 chains. Longest chain 21 peptides. Score 0.567 Round 5: 291 peptides, 37 chains. Longest chain 18 peptides. Score 0.560 Taking the results from Round 2 Chains 29, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 7232 restraints for refining 3264 atoms. 6321 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2303 (Rfree = 0.000) for 3264 atoms. Found 13 (17 requested) and removed 20 (8 requested) atoms. Cycle 12: After refmac, R = 0.2144 (Rfree = 0.000) for 3231 atoms. Found 12 (17 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.1870 (Rfree = 0.000) for 3207 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1777 (Rfree = 0.000) for 3191 atoms. Found 1 (17 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2057 (Rfree = 0.000) for 3172 atoms. Found 8 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.05 Search for helices and strands: 0 residues in 0 chains, 3279 seeds are put forward Round 1: 253 peptides, 43 chains. Longest chain 15 peptides. Score 0.406 Round 2: 272 peptides, 39 chains. Longest chain 22 peptides. Score 0.497 Round 3: 285 peptides, 41 chains. Longest chain 15 peptides. Score 0.507 Round 4: 292 peptides, 36 chains. Longest chain 31 peptides. Score 0.572 Round 5: 292 peptides, 41 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 4 Chains 38, Residues 256, Estimated correctness of the model 0.0 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 6688 restraints for refining 3264 atoms. 5545 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2588 (Rfree = 0.000) for 3264 atoms. Found 4 (17 requested) and removed 30 (8 requested) atoms. Cycle 17: After refmac, R = 0.2459 (Rfree = 0.000) for 3210 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 18: After refmac, R = 0.2178 (Rfree = 0.000) for 3178 atoms. Found 6 (17 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.2107 (Rfree = 0.000) for 3162 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2126 (Rfree = 0.000) for 3142 atoms. Found 10 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.05 Search for helices and strands: 0 residues in 0 chains, 3287 seeds are put forward Round 1: 248 peptides, 41 chains. Longest chain 12 peptides. Score 0.416 Round 2: 273 peptides, 37 chains. Longest chain 24 peptides. Score 0.520 Round 3: 271 peptides, 39 chains. Longest chain 14 peptides. Score 0.495 Round 4: 258 peptides, 35 chains. Longest chain 17 peptides. Score 0.506 Round 5: 276 peptides, 37 chains. Longest chain 17 peptides. Score 0.527 Taking the results from Round 5 Chains 41, Residues 239, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 7016 restraints for refining 3264 atoms. 6002 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2599 (Rfree = 0.000) for 3264 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.2437 (Rfree = 0.000) for 3220 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2328 (Rfree = 0.000) for 3198 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2003 (Rfree = 0.000) for 3189 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.2132 (Rfree = 0.000) for 3168 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.08 Search for helices and strands: 0 residues in 0 chains, 3264 seeds are put forward Round 1: 232 peptides, 44 chains. Longest chain 10 peptides. Score 0.337 Round 2: 256 peptides, 42 chains. Longest chain 14 peptides. Score 0.425 Round 3: 274 peptides, 38 chains. Longest chain 19 peptides. Score 0.512 Round 4: 270 peptides, 40 chains. Longest chain 18 peptides. Score 0.482 Round 5: 259 peptides, 36 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 3 Chains 38, Residues 236, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 6958 restraints for refining 3263 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2644 (Rfree = 0.000) for 3263 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.2464 (Rfree = 0.000) for 3216 atoms. Found 10 (17 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2391 (Rfree = 0.000) for 3187 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.2368 (Rfree = 0.000) for 3165 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2281 (Rfree = 0.000) for 3152 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.07 Search for helices and strands: 0 residues in 0 chains, 3245 seeds are put forward Round 1: 224 peptides, 42 chains. Longest chain 12 peptides. Score 0.339 Round 2: 252 peptides, 43 chains. Longest chain 12 peptides. Score 0.403 Round 3: 270 peptides, 43 chains. Longest chain 21 peptides. Score 0.450 Round 4: 273 peptides, 42 chains. Longest chain 14 peptides. Score 0.468 Round 5: 271 peptides, 41 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 5 Chains 41, Residues 230, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 7335 restraints for refining 3264 atoms. 6429 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2801 (Rfree = 0.000) for 3264 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2618 (Rfree = 0.000) for 3206 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.2522 (Rfree = 0.000) for 3184 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.2344 (Rfree = 0.000) for 3168 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.2367 (Rfree = 0.000) for 3161 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.06 Search for helices and strands: 0 residues in 0 chains, 3263 seeds are put forward Round 1: 229 peptides, 42 chains. Longest chain 10 peptides. Score 0.353 Round 2: 220 peptides, 37 chains. Longest chain 9 peptides. Score 0.388 Round 3: 245 peptides, 37 chains. Longest chain 17 peptides. Score 0.453 Round 4: 239 peptides, 37 chains. Longest chain 17 peptides. Score 0.438 Round 5: 253 peptides, 38 chains. Longest chain 14 peptides. Score 0.462 Taking the results from Round 5 Chains 38, Residues 215, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 7328 restraints for refining 3264 atoms. 6496 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2352 (Rfree = 0.000) for 3264 atoms. Found 1 (17 requested) and removed 16 (8 requested) atoms. Cycle 37: After refmac, R = 0.2260 (Rfree = 0.000) for 3223 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.2238 (Rfree = 0.000) for 3205 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2153 (Rfree = 0.000) for 3193 atoms. Found 8 (17 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.1863 (Rfree = 0.000) for 3184 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.05 Search for helices and strands: 0 residues in 0 chains, 3295 seeds are put forward Round 1: 221 peptides, 44 chains. Longest chain 12 peptides. Score 0.306 Round 2: 219 peptides, 35 chains. Longest chain 15 peptides. Score 0.409 Round 3: 240 peptides, 37 chains. Longest chain 20 peptides. Score 0.440 Round 4: 239 peptides, 39 chains. Longest chain 15 peptides. Score 0.415 Round 5: 250 peptides, 37 chains. Longest chain 15 peptides. Score 0.465 Taking the results from Round 5 Chains 37, Residues 213, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6212 reflections ( 99.04 % complete ) and 7081 restraints for refining 3261 atoms. 6156 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2371 (Rfree = 0.000) for 3261 atoms. Found 11 (17 requested) and removed 15 (8 requested) atoms. Cycle 42: After refmac, R = 0.2259 (Rfree = 0.000) for 3229 atoms. Found 7 (17 requested) and removed 18 (8 requested) atoms. Cycle 43: After refmac, R = 0.2256 (Rfree = 0.000) for 3200 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.2225 (Rfree = 0.000) for 3189 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2026 (Rfree = 0.000) for 3186 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.06 Search for helices and strands: 0 residues in 0 chains, 3282 seeds are put forward Round 1: 194 peptides, 35 chains. Longest chain 10 peptides. Score 0.339 Round 2: 197 peptides, 30 chains. Longest chain 12 peptides. Score 0.409 Round 3: 215 peptides, 32 chains. Longest chain 15 peptides. Score 0.433 Round 4: 217 peptides, 36 chains. Longest chain 15 peptides. Score 0.391 Round 5: 228 peptides, 33 chains. Longest chain 13 peptides. Score 0.455 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 195, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vpb-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (195 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6212 reflections ( 99.04 % complete ) and 7184 restraints for refining 3264 atoms. 6369 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2350 (Rfree = 0.000) for 3264 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2156 (Rfree = 0.000) for 3226 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2160 (Rfree = 0.000) for 3194 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2179 (Rfree = 0.000) for 3171 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:19:45 GMT 2018 Job finished. TimeTaking 56.92 Used memory is bytes: 9862752