null 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 1vl0-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-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/1vl0-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-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/1vl0-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-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 695 and 0 Target number of residues in the AU: 695 Target solvent content: 0.6424 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-3.8-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: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 7008 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 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: 29.987 3.800 Wilson plot Bfac: 73.35 10604 reflections ( 98.86 % complete ) and 0 restraints for refining 7774 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3794 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3565 (Rfree = 0.000) for 7774 atoms. Found 42 (42 requested) and removed 78 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 7780 seeds are put forward NCS extension: 0 residues added, 7780 seeds are put forward Round 1: 193 peptides, 43 chains. Longest chain 9 peptides. Score 0.213 Round 2: 257 peptides, 54 chains. Longest chain 9 peptides. Score 0.249 Round 3: 292 peptides, 59 chains. Longest chain 10 peptides. Score 0.275 Round 4: 330 peptides, 61 chains. Longest chain 10 peptides. Score 0.326 Round 5: 318 peptides, 61 chains. Longest chain 12 peptides. Score 0.306 Taking the results from Round 4 Chains 61, Residues 269, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14634 restraints for refining 6339 atoms. 13589 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3121 (Rfree = 0.000) for 6339 atoms. Found 34 (34 requested) and removed 36 (17 requested) atoms. Cycle 2: After refmac, R = 0.2809 (Rfree = 0.000) for 6245 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 3: After refmac, R = 0.2399 (Rfree = 0.000) for 6194 atoms. Found 11 (34 requested) and removed 24 (17 requested) atoms. Cycle 4: After refmac, R = 0.2270 (Rfree = 0.000) for 6140 atoms. Found 11 (33 requested) and removed 21 (16 requested) atoms. Cycle 5: After refmac, R = 0.2214 (Rfree = 0.000) for 6101 atoms. Found 9 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 6213 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 6222 seeds are put forward Round 1: 269 peptides, 59 chains. Longest chain 8 peptides. Score 0.232 Round 2: 359 peptides, 66 chains. Longest chain 13 peptides. Score 0.339 Round 3: 360 peptides, 64 chains. Longest chain 11 peptides. Score 0.354 Round 4: 373 peptides, 65 chains. Longest chain 12 peptides. Score 0.369 Round 5: 400 peptides, 68 chains. Longest chain 15 peptides. Score 0.391 Taking the results from Round 5 Chains 68, Residues 332, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13427 restraints for refining 6018 atoms. 12146 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2652 (Rfree = 0.000) for 6018 atoms. Found 19 (33 requested) and removed 54 (16 requested) atoms. Cycle 7: After refmac, R = 0.2427 (Rfree = 0.000) for 5921 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 8: After refmac, R = 0.2366 (Rfree = 0.000) for 5880 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 9: After refmac, R = 0.2409 (Rfree = 0.000) for 5858 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 10: After refmac, R = 0.2346 (Rfree = 0.000) for 5834 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.20 Search for helices and strands: 0 residues in 0 chains, 5968 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5989 seeds are put forward Round 1: 350 peptides, 75 chains. Longest chain 11 peptides. Score 0.258 Round 2: 411 peptides, 75 chains. Longest chain 11 peptides. Score 0.360 Round 3: 394 peptides, 70 chains. Longest chain 12 peptides. Score 0.368 Round 4: 421 peptides, 78 chains. Longest chain 11 peptides. Score 0.356 Round 5: 429 peptides, 78 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 5 Chains 78, Residues 351, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13756 restraints for refining 6284 atoms. 12390 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2294 (Rfree = 0.000) for 6284 atoms. Found 22 (34 requested) and removed 55 (17 requested) atoms. Cycle 12: After refmac, R = 0.2093 (Rfree = 0.000) for 6189 atoms. Found 15 (34 requested) and removed 29 (17 requested) atoms. Cycle 13: After refmac, R = 0.2046 (Rfree = 0.000) for 6154 atoms. Found 9 (33 requested) and removed 23 (16 requested) atoms. Cycle 14: After refmac, R = 0.2030 (Rfree = 0.000) for 6137 atoms. Found 5 (33 requested) and removed 18 (16 requested) atoms. Cycle 15: After refmac, R = 0.2021 (Rfree = 0.000) for 6121 atoms. Found 8 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 6175 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6193 seeds are put forward Round 1: 359 peptides, 75 chains. Longest chain 9 peptides. Score 0.274 Round 2: 399 peptides, 68 chains. Longest chain 12 peptides. Score 0.389 Round 3: 400 peptides, 69 chains. Longest chain 14 peptides. Score 0.384 Round 4: 438 peptides, 73 chains. Longest chain 15 peptides. Score 0.416 Round 5: 409 peptides, 66 chains. Longest chain 15 peptides. Score 0.418 Taking the results from Round 5 Chains 66, Residues 343, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14409 restraints for refining 6339 atoms. 13080 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2338 (Rfree = 0.000) for 6339 atoms. Found 34 (34 requested) and removed 38 (17 requested) atoms. Cycle 17: After refmac, R = 0.2382 (Rfree = 0.000) for 6291 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 18: After refmac, R = 0.2366 (Rfree = 0.000) for 6264 atoms. Found 34 (34 requested) and removed 35 (17 requested) atoms. Cycle 19: After refmac, R = 0.2196 (Rfree = 0.000) for 6239 atoms. Found 29 (34 requested) and removed 29 (17 requested) atoms. Cycle 20: After refmac, R = 0.2243 (Rfree = 0.000) for 6217 atoms. Found 31 (34 requested) and removed 34 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 6321 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6335 seeds are put forward Round 1: 315 peptides, 68 chains. Longest chain 10 peptides. Score 0.248 Round 2: 345 peptides, 62 chains. Longest chain 17 peptides. Score 0.344 Round 3: 368 peptides, 64 chains. Longest chain 15 peptides. Score 0.367 Round 4: 374 peptides, 61 chains. Longest chain 19 peptides. Score 0.398 Round 5: 367 peptides, 60 chains. Longest chain 15 peptides. Score 0.394 Taking the results from Round 4 Chains 63, Residues 313, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14161 restraints for refining 6337 atoms. 12908 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2387 (Rfree = 0.000) for 6337 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 22: After refmac, R = 0.2326 (Rfree = 0.000) for 6278 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 23: After refmac, R = 0.2237 (Rfree = 0.000) for 6249 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 24: After refmac, R = 0.2231 (Rfree = 0.000) for 6228 atoms. Found 29 (34 requested) and removed 28 (17 requested) atoms. Cycle 25: After refmac, R = 0.2252 (Rfree = 0.000) for 6215 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.21 Search for helices and strands: 0 residues in 0 chains, 6294 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6314 seeds are put forward Round 1: 284 peptides, 59 chains. Longest chain 12 peptides. Score 0.260 Round 2: 361 peptides, 68 chains. Longest chain 12 peptides. Score 0.328 Round 3: 380 peptides, 72 chains. Longest chain 12 peptides. Score 0.331 Round 4: 382 peptides, 68 chains. Longest chain 11 peptides. Score 0.362 Round 5: 393 peptides, 68 chains. Longest chain 12 peptides. Score 0.380 Taking the results from Round 5 Chains 68, Residues 325, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13772 restraints for refining 6338 atoms. 12450 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2406 (Rfree = 0.000) for 6338 atoms. Found 34 (34 requested) and removed 41 (17 requested) atoms. Cycle 27: After refmac, R = 0.2332 (Rfree = 0.000) for 6279 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 6245 atoms. Found 34 (34 requested) and removed 39 (17 requested) atoms. Cycle 29: After refmac, R = 0.2286 (Rfree = 0.000) for 6216 atoms. Found 34 (34 requested) and removed 36 (17 requested) atoms. Cycle 30: After refmac, R = 0.2157 (Rfree = 0.000) for 6199 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 6306 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6324 seeds are put forward Round 1: 328 peptides, 70 chains. Longest chain 8 peptides. Score 0.256 Round 2: 354 peptides, 65 chains. Longest chain 11 peptides. Score 0.338 Round 3: 373 peptides, 66 chains. Longest chain 12 peptides. Score 0.362 Round 4: 378 peptides, 65 chains. Longest chain 13 peptides. Score 0.377 Round 5: 395 peptides, 59 chains. Longest chain 19 peptides. Score 0.443 Taking the results from Round 5 Chains 60, Residues 336, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13822 restraints for refining 6337 atoms. 12496 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2300 (Rfree = 0.000) for 6337 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 32: After refmac, R = 0.2300 (Rfree = 0.000) for 6304 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 33: After refmac, R = 0.2232 (Rfree = 0.000) for 6273 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 34: After refmac, R = 0.2212 (Rfree = 0.000) for 6268 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 35: After refmac, R = 0.2276 (Rfree = 0.000) for 6253 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 6361 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6375 seeds are put forward Round 1: 301 peptides, 66 chains. Longest chain 8 peptides. Score 0.238 Round 2: 324 peptides, 58 chains. Longest chain 18 peptides. Score 0.338 Round 3: 336 peptides, 60 chains. Longest chain 12 peptides. Score 0.343 Round 4: 352 peptides, 60 chains. Longest chain 13 peptides. Score 0.370 Round 5: 341 peptides, 61 chains. Longest chain 13 peptides. Score 0.345 Taking the results from Round 4 Chains 61, Residues 292, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14165 restraints for refining 6338 atoms. 12993 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2508 (Rfree = 0.000) for 6338 atoms. Found 34 (34 requested) and removed 44 (17 requested) atoms. Cycle 37: After refmac, R = 0.2320 (Rfree = 0.000) for 6287 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 38: After refmac, R = 0.2198 (Rfree = 0.000) for 6262 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 39: After refmac, R = 0.2124 (Rfree = 0.000) for 6247 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 40: After refmac, R = 0.2110 (Rfree = 0.000) for 6240 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 6315 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6330 seeds are put forward Round 1: 243 peptides, 54 chains. Longest chain 7 peptides. Score 0.222 Round 2: 285 peptides, 52 chains. Longest chain 14 peptides. Score 0.316 Round 3: 306 peptides, 58 chains. Longest chain 10 peptides. Score 0.307 Round 4: 296 peptides, 50 chains. Longest chain 11 peptides. Score 0.350 Round 5: 320 peptides, 52 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 5 Chains 52, Residues 268, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14017 restraints for refining 6338 atoms. 12951 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2386 (Rfree = 0.000) for 6338 atoms. Found 34 (34 requested) and removed 51 (17 requested) atoms. Cycle 42: After refmac, R = 0.2228 (Rfree = 0.000) for 6295 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 43: After refmac, R = 0.2205 (Rfree = 0.000) for 6276 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 44: After refmac, R = 0.2174 (Rfree = 0.000) for 6272 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 45: After refmac, R = 0.2112 (Rfree = 0.000) for 6265 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 6308 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6323 seeds are put forward Round 1: 268 peptides, 57 chains. Longest chain 9 peptides. Score 0.246 Round 2: 290 peptides, 56 chains. Longest chain 11 peptides. Score 0.294 Round 3: 270 peptides, 48 chains. Longest chain 10 peptides. Score 0.320 Round 4: 274 peptides, 48 chains. Longest chain 10 peptides. Score 0.327 Round 5: 274 peptides, 49 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 226, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input Building loops using Loopy2018 48 chains (226 residues) following loop building 4 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10604 reflections ( 98.86 % complete ) and 14556 restraints for refining 6339 atoms. 13666 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2228 (Rfree = 0.000) for 6339 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2234 (Rfree = 0.000) for 6301 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2261 (Rfree = 0.000) for 6271 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2134 (Rfree = 0.000) for 6236 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:59:37 GMT 2018 Job finished. TimeTaking 91.66 Used memory is bytes: 20263144