Mon 24 Dec 00:47:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl0-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:47:33 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 7722 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3814 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3534 (Rfree = 0.000) for 7722 atoms. Found 42 (42 requested) and removed 92 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 7725 seeds are put forward NCS extension: 0 residues added, 7725 seeds are put forward Round 1: 152 peptides, 34 chains. Longest chain 9 peptides. Score 0.206 Round 2: 219 peptides, 48 chains. Longest chain 7 peptides. Score 0.224 Round 3: 276 peptides, 57 chains. Longest chain 13 peptides. Score 0.261 Round 4: 289 peptides, 56 chains. Longest chain 10 peptides. Score 0.292 Round 5: 297 peptides, 59 chains. Longest chain 10 peptides. Score 0.284 Taking the results from Round 4 Chains 56, Residues 233, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14935 restraints for refining 6339 atoms. 14032 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3094 (Rfree = 0.000) for 6339 atoms. Found 30 (34 requested) and removed 38 (17 requested) atoms. Cycle 2: After refmac, R = 0.3031 (Rfree = 0.000) for 6235 atoms. Found 34 (34 requested) and removed 43 (17 requested) atoms. Cycle 3: After refmac, R = 0.2981 (Rfree = 0.000) for 6159 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 4: After refmac, R = 0.3003 (Rfree = 0.000) for 6117 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. Cycle 5: After refmac, R = 0.2802 (Rfree = 0.000) for 6091 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.20 Search for helices and strands: 0 residues in 0 chains, 6200 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 6203 seeds are put forward Round 1: 245 peptides, 53 chains. Longest chain 10 peptides. Score 0.234 Round 2: 345 peptides, 66 chains. Longest chain 12 peptides. Score 0.315 Round 3: 384 peptides, 71 chains. Longest chain 10 peptides. Score 0.345 Round 4: 371 peptides, 62 chains. Longest chain 21 peptides. Score 0.386 Round 5: 387 peptides, 64 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 5 Chains 64, Residues 323, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 12766 restraints for refining 5821 atoms. 11523 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2799 (Rfree = 0.000) for 5821 atoms. Found 32 (32 requested) and removed 48 (16 requested) atoms. Cycle 7: After refmac, R = 0.2734 (Rfree = 0.000) for 5731 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 8: After refmac, R = 0.2658 (Rfree = 0.000) for 5685 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 9: After refmac, R = 0.2520 (Rfree = 0.000) for 5644 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 10: After refmac, R = 0.2560 (Rfree = 0.000) for 5627 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 5729 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5744 seeds are put forward Round 1: 354 peptides, 71 chains. Longest chain 11 peptides. Score 0.294 Round 2: 431 peptides, 77 chains. Longest chain 12 peptides. Score 0.379 Round 3: 421 peptides, 68 chains. Longest chain 20 peptides. Score 0.423 Round 4: 435 peptides, 73 chains. Longest chain 18 peptides. Score 0.411 Round 5: 445 peptides, 70 chains. Longest chain 18 peptides. Score 0.445 Taking the results from Round 5 Chains 72, Residues 375, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13245 restraints for refining 6181 atoms. 11727 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2651 (Rfree = 0.000) for 6181 atoms. Found 34 (34 requested) and removed 75 (17 requested) atoms. Cycle 12: After refmac, R = 0.2535 (Rfree = 0.000) for 6066 atoms. Found 33 (33 requested) and removed 49 (16 requested) atoms. Cycle 13: After refmac, R = 0.2408 (Rfree = 0.000) for 6016 atoms. Found 33 (33 requested) and removed 35 (16 requested) atoms. Cycle 14: After refmac, R = 0.2482 (Rfree = 0.000) for 5986 atoms. Found 33 (33 requested) and removed 33 (16 requested) atoms. Cycle 15: After refmac, R = 0.2249 (Rfree = 0.000) for 5967 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 6100 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 6121 seeds are put forward Round 1: 343 peptides, 69 chains. Longest chain 10 peptides. Score 0.290 Round 2: 381 peptides, 63 chains. Longest chain 13 peptides. Score 0.395 Round 3: 398 peptides, 65 chains. Longest chain 19 peptides. Score 0.408 Round 4: 400 peptides, 64 chains. Longest chain 15 peptides. Score 0.418 Round 5: 406 peptides, 69 chains. Longest chain 14 peptides. Score 0.393 Taking the results from Round 4 Chains 64, Residues 336, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14116 restraints for refining 6338 atoms. 12817 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2244 (Rfree = 0.000) for 6338 atoms. Found 30 (34 requested) and removed 55 (17 requested) atoms. Cycle 17: After refmac, R = 0.2270 (Rfree = 0.000) for 6270 atoms. Found 34 (34 requested) and removed 35 (17 requested) atoms. Cycle 18: After refmac, R = 0.2279 (Rfree = 0.000) for 6248 atoms. Found 34 (34 requested) and removed 36 (17 requested) atoms. Cycle 19: After refmac, R = 0.2308 (Rfree = 0.000) for 6230 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 20: After refmac, R = 0.2295 (Rfree = 0.000) for 6208 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 6335 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6357 seeds are put forward Round 1: 304 peptides, 62 chains. Longest chain 10 peptides. Score 0.273 Round 2: 364 peptides, 68 chains. Longest chain 10 peptides. Score 0.333 Round 3: 385 peptides, 67 chains. Longest chain 11 peptides. Score 0.374 Round 4: 378 peptides, 58 chains. Longest chain 16 peptides. Score 0.424 Round 5: 372 peptides, 61 chains. Longest chain 18 peptides. Score 0.395 Taking the results from Round 4 Chains 58, Residues 320, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14193 restraints for refining 6338 atoms. 12930 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2388 (Rfree = 0.000) for 6338 atoms. Found 27 (34 requested) and removed 39 (17 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 6277 atoms. Found 34 (34 requested) and removed 34 (17 requested) atoms. Cycle 23: After refmac, R = 0.2171 (Rfree = 0.000) for 6241 atoms. Found 26 (34 requested) and removed 25 (17 requested) atoms. Cycle 24: After refmac, R = 0.2278 (Rfree = 0.000) for 6223 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 25: After refmac, R = 0.2060 (Rfree = 0.000) for 6217 atoms. Found 34 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 6332 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6353 seeds are put forward Round 1: 324 peptides, 65 chains. Longest chain 13 peptides. Score 0.286 Round 2: 374 peptides, 66 chains. Longest chain 18 peptides. Score 0.363 Round 3: 396 peptides, 65 chains. Longest chain 20 peptides. Score 0.405 Round 4: 395 peptides, 67 chains. Longest chain 17 peptides. Score 0.390 Round 5: 372 peptides, 62 chains. Longest chain 21 peptides. Score 0.388 Taking the results from Round 3 Chains 65, Residues 331, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 14163 restraints for refining 6322 atoms. 12904 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2163 (Rfree = 0.000) for 6322 atoms. Found 26 (34 requested) and removed 48 (17 requested) atoms. Cycle 27: After refmac, R = 0.2113 (Rfree = 0.000) for 6245 atoms. Found 34 (34 requested) and removed 34 (17 requested) atoms. Cycle 28: After refmac, R = 0.2227 (Rfree = 0.000) for 6224 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 29: After refmac, R = 0.2184 (Rfree = 0.000) for 6218 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 30: After refmac, R = 0.2210 (Rfree = 0.000) for 6203 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 6305 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 6327 seeds are put forward Round 1: 302 peptides, 61 chains. Longest chain 16 peptides. Score 0.277 Round 2: 350 peptides, 63 chains. Longest chain 16 peptides. Score 0.345 Round 3: 356 peptides, 60 chains. Longest chain 16 peptides. Score 0.376 Round 4: 367 peptides, 62 chains. Longest chain 16 peptides. Score 0.380 Round 5: 365 peptides, 58 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 5 Chains 59, Residues 307, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13988 restraints for refining 6339 atoms. 12766 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2231 (Rfree = 0.000) for 6339 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 32: After refmac, R = 0.2171 (Rfree = 0.000) for 6301 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 33: After refmac, R = 0.2173 (Rfree = 0.000) for 6280 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 34: After refmac, R = 0.2218 (Rfree = 0.000) for 6271 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 35: After refmac, R = 0.2199 (Rfree = 0.000) for 6260 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 6362 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6383 seeds are put forward Round 1: 270 peptides, 58 chains. Longest chain 8 peptides. Score 0.242 Round 2: 317 peptides, 54 chains. Longest chain 16 peptides. Score 0.356 Round 3: 334 peptides, 60 chains. Longest chain 16 peptides. Score 0.340 Round 4: 342 peptides, 60 chains. Longest chain 16 peptides. Score 0.353 Round 5: 326 peptides, 58 chains. Longest chain 13 peptides. Score 0.341 Taking the results from Round 2 Chains 54, Residues 263, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13954 restraints for refining 6260 atoms. 12926 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2191 (Rfree = 0.000) for 6260 atoms. Found 34 (34 requested) and removed 41 (17 requested) atoms. Cycle 37: After refmac, R = 0.2237 (Rfree = 0.000) for 6230 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 38: After refmac, R = 0.2260 (Rfree = 0.000) for 6215 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 39: After refmac, R = 0.2272 (Rfree = 0.000) for 6201 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 40: After refmac, R = 0.2267 (Rfree = 0.000) for 6192 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 6288 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6316 seeds are put forward Round 1: 251 peptides, 54 chains. Longest chain 8 peptides. Score 0.238 Round 2: 289 peptides, 51 chains. Longest chain 11 peptides. Score 0.330 Round 3: 300 peptides, 51 chains. Longest chain 13 peptides. Score 0.349 Round 4: 295 peptides, 50 chains. Longest chain 11 peptides. Score 0.348 Round 5: 286 peptides, 49 chains. Longest chain 12 peptides. Score 0.340 Taking the results from Round 3 Chains 51, Residues 249, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10604 reflections ( 98.86 % complete ) and 13803 restraints for refining 6264 atoms. 12826 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2180 (Rfree = 0.000) for 6264 atoms. Found 34 (34 requested) and removed 39 (17 requested) atoms. Cycle 42: After refmac, R = 0.2212 (Rfree = 0.000) for 6226 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 43: After refmac, R = 0.2212 (Rfree = 0.000) for 6215 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 44: After refmac, R = 0.2224 (Rfree = 0.000) for 6195 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 45: After refmac, R = 0.2091 (Rfree = 0.000) for 6181 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 6243 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6263 seeds are put forward Round 1: 263 peptides, 57 chains. Longest chain 10 peptides. Score 0.237 Round 2: 275 peptides, 54 chains. Longest chain 10 peptides. Score 0.282 Round 3: 279 peptides, 48 chains. Longest chain 12 peptides. Score 0.336 Round 4: 301 peptides, 53 chains. Longest chain 11 peptides. Score 0.336 Round 5: 313 peptides, 54 chains. Longest chain 13 peptides. Score 0.349 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 259, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (259 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10604 reflections ( 98.86 % complete ) and 13678 restraints for refining 6228 atoms. 12667 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2259 (Rfree = 0.000) for 6228 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2359 (Rfree = 0.000) for 6169 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2177 (Rfree = 0.000) for 6121 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2285 (Rfree = 0.000) for 6085 atoms. TimeTaking 59.68