Mon 24 Dec 00:52:03 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 1vr0-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-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/1vr0-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-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 00:52:07 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-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 462 and 0 Target number of residues in the AU: 462 Target solvent content: 0.6587 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-4.0-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: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.70 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: 226.759 4.000 Wilson plot Bfac: 83.88 6637 reflections ( 99.51 % complete ) and 0 restraints for refining 6556 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3374 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3310 (Rfree = 0.000) for 6556 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 4.07 Search for helices and strands: 0 residues in 0 chains, 6673 seeds are put forward NCS extension: 0 residues added, 6673 seeds are put forward Round 1: 249 peptides, 52 chains. Longest chain 8 peptides. Score 0.274 Round 2: 302 peptides, 54 chains. Longest chain 16 peptides. Score 0.379 Round 3: 327 peptides, 53 chains. Longest chain 17 peptides. Score 0.442 Round 4: 359 peptides, 54 chains. Longest chain 17 peptides. Score 0.498 Round 5: 375 peptides, 53 chains. Longest chain 18 peptides. Score 0.536 Taking the results from Round 5 Chains 53, Residues 322, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12644 restraints for refining 5353 atoms. 11409 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2403 (Rfree = 0.000) for 5353 atoms. Found 20 (25 requested) and removed 41 (12 requested) atoms. Cycle 2: After refmac, R = 0.2252 (Rfree = 0.000) for 5258 atoms. Found 24 (25 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2321 (Rfree = 0.000) for 5214 atoms. Found 24 (24 requested) and removed 51 (12 requested) atoms. Cycle 4: After refmac, R = 0.2227 (Rfree = 0.000) for 5155 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 5: After refmac, R = 0.2063 (Rfree = 0.000) for 5128 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 5360 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 5380 seeds are put forward Round 1: 284 peptides, 53 chains. Longest chain 11 peptides. Score 0.348 Round 2: 330 peptides, 56 chains. Longest chain 16 peptides. Score 0.421 Round 3: 341 peptides, 52 chains. Longest chain 18 peptides. Score 0.480 Round 4: 338 peptides, 54 chains. Longest chain 14 peptides. Score 0.456 Round 5: 359 peptides, 55 chains. Longest chain 16 peptides. Score 0.489 Taking the results from Round 5 Chains 56, Residues 304, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12641 restraints for refining 5354 atoms. 11401 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2088 (Rfree = 0.000) for 5354 atoms. Found 13 (25 requested) and removed 56 (12 requested) atoms. Cycle 7: After refmac, R = 0.2212 (Rfree = 0.000) for 5280 atoms. Found 25 (25 requested) and removed 48 (12 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2222 (Rfree = 0.000) for 5238 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 9: After refmac, R = 0.2089 (Rfree = 0.000) for 5207 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 10: After refmac, R = 0.2032 (Rfree = 0.000) for 5183 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.98 Search for helices and strands: 0 residues in 0 chains, 5400 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 5427 seeds are put forward Round 1: 304 peptides, 61 chains. Longest chain 11 peptides. Score 0.316 Round 2: 334 peptides, 52 chains. Longest chain 18 peptides. Score 0.466 Round 3: 344 peptides, 53 chains. Longest chain 20 peptides. Score 0.477 Round 4: 347 peptides, 55 chains. Longest chain 14 peptides. Score 0.465 Round 5: 335 peptides, 50 chains. Longest chain 15 peptides. Score 0.485 Taking the results from Round 5 Chains 51, Residues 285, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12846 restraints for refining 5354 atoms. 11727 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2268 (Rfree = 0.000) for 5354 atoms. Found 24 (25 requested) and removed 40 (12 requested) atoms. Cycle 12: After refmac, R = 0.2109 (Rfree = 0.000) for 5307 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 13: After refmac, R = 0.1607 (Rfree = 0.000) for 5274 atoms. Found 7 (25 requested) and removed 22 (12 requested) atoms. Cycle 14: After refmac, R = 0.1656 (Rfree = 0.000) for 5243 atoms. Found 12 (24 requested) and removed 18 (12 requested) atoms. Cycle 15: After refmac, R = 0.1996 (Rfree = 0.000) for 5232 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 5442 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5459 seeds are put forward Round 1: 274 peptides, 49 chains. Longest chain 13 peptides. Score 0.364 Round 2: 305 peptides, 48 chains. Longest chain 14 peptides. Score 0.442 Round 3: 312 peptides, 47 chains. Longest chain 22 peptides. Score 0.466 Round 4: 339 peptides, 44 chains. Longest chain 21 peptides. Score 0.544 Round 5: 338 peptides, 46 chains. Longest chain 17 peptides. Score 0.525 Taking the results from Round 4 Chains 44, Residues 295, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12467 restraints for refining 5354 atoms. 11235 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2059 (Rfree = 0.000) for 5354 atoms. Found 22 (25 requested) and removed 32 (12 requested) atoms. Cycle 17: After refmac, R = 0.2216 (Rfree = 0.000) for 5313 atoms. Found 25 (25 requested) and removed 42 (12 requested) atoms. Cycle 18: After refmac, R = 0.2079 (Rfree = 0.000) for 5273 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 19: After refmac, R = 0.1532 (Rfree = 0.000) for 5250 atoms. Found 8 (25 requested) and removed 25 (12 requested) atoms. Cycle 20: After refmac, R = 0.1565 (Rfree = 0.000) for 5229 atoms. Found 8 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.97 Search for helices and strands: 0 residues in 0 chains, 5444 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 5472 seeds are put forward Round 1: 270 peptides, 53 chains. Longest chain 10 peptides. Score 0.315 Round 2: 301 peptides, 50 chains. Longest chain 14 peptides. Score 0.415 Round 3: 302 peptides, 49 chains. Longest chain 16 peptides. Score 0.426 Round 4: 308 peptides, 50 chains. Longest chain 17 peptides. Score 0.430 Round 5: 310 peptides, 48 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 5 Chains 48, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12853 restraints for refining 5352 atoms. 11853 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2116 (Rfree = 0.000) for 5352 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 22: After refmac, R = 0.2128 (Rfree = 0.000) for 5331 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 23: After refmac, R = 0.2140 (Rfree = 0.000) for 5302 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 24: After refmac, R = 0.2014 (Rfree = 0.000) for 5277 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 25: After refmac, R = 0.1832 (Rfree = 0.000) for 5266 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.95 Search for helices and strands: 0 residues in 0 chains, 5489 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 5511 seeds are put forward Round 1: 240 peptides, 52 chains. Longest chain 8 peptides. Score 0.251 Round 2: 291 peptides, 51 chains. Longest chain 14 peptides. Score 0.383 Round 3: 279 peptides, 47 chains. Longest chain 13 peptides. Score 0.395 Round 4: 264 peptides, 41 chains. Longest chain 12 peptides. Score 0.420 Round 5: 273 peptides, 43 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 5 Chains 43, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 13042 restraints for refining 5353 atoms. 12165 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1992 (Rfree = 0.000) for 5353 atoms. Found 25 (25 requested) and removed 39 (12 requested) atoms. Cycle 27: After refmac, R = 0.2088 (Rfree = 0.000) for 5320 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 5289 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 29: After refmac, R = 0.2026 (Rfree = 0.000) for 5265 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 30: After refmac, R = 0.2001 (Rfree = 0.000) for 5257 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.98 Search for helices and strands: 0 residues in 0 chains, 5415 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5434 seeds are put forward Round 1: 203 peptides, 42 chains. Longest chain 9 peptides. Score 0.264 Round 2: 236 peptides, 43 chains. Longest chain 10 peptides. Score 0.336 Round 3: 239 peptides, 42 chains. Longest chain 12 peptides. Score 0.353 Round 4: 251 peptides, 42 chains. Longest chain 13 peptides. Score 0.381 Round 5: 247 peptides, 37 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 5 Chains 37, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12958 restraints for refining 5345 atoms. 12155 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2050 (Rfree = 0.000) for 5345 atoms. Found 22 (25 requested) and removed 48 (12 requested) atoms. Cycle 32: After refmac, R = 0.2092 (Rfree = 0.000) for 5301 atoms. Found 25 (25 requested) and removed 38 (12 requested) atoms. Cycle 33: After refmac, R = 0.1821 (Rfree = 0.000) for 5282 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. Cycle 34: After refmac, R = 0.1345 (Rfree = 0.000) for 5266 atoms. Found 9 (25 requested) and removed 18 (12 requested) atoms. Cycle 35: After refmac, R = 0.1240 (Rfree = 0.000) for 5253 atoms. Found 0 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 5421 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5438 seeds are put forward Round 1: 239 peptides, 50 chains. Longest chain 8 peptides. Score 0.270 Round 2: 260 peptides, 49 chains. Longest chain 14 peptides. Score 0.332 Round 3: 258 peptides, 46 chains. Longest chain 10 peptides. Score 0.357 Round 4: 248 peptides, 43 chains. Longest chain 11 peptides. Score 0.364 Round 5: 252 peptides, 39 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Chains 40, Residues 213, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12697 restraints for refining 5353 atoms. 11834 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2077 (Rfree = 0.000) for 5353 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 5320 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.2146 (Rfree = 0.000) for 5297 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 39: After refmac, R = 0.2072 (Rfree = 0.000) for 5268 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 40: After refmac, R = 0.1940 (Rfree = 0.000) for 5249 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.97 Search for helices and strands: 0 residues in 0 chains, 5411 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5426 seeds are put forward Round 1: 170 peptides, 38 chains. Longest chain 7 peptides. Score 0.220 Round 2: 216 peptides, 40 chains. Longest chain 13 peptides. Score 0.319 Round 3: 230 peptides, 42 chains. Longest chain 11 peptides. Score 0.332 Round 4: 266 peptides, 49 chains. Longest chain 10 peptides. Score 0.346 Round 5: 254 peptides, 44 chains. Longest chain 16 peptides. Score 0.368 Taking the results from Round 5 Chains 44, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12542 restraints for refining 5247 atoms. 11746 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1877 (Rfree = 0.000) for 5247 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 42: After refmac, R = 0.1937 (Rfree = 0.000) for 5219 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 43: After refmac, R = 0.1960 (Rfree = 0.000) for 5204 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 44: After refmac, R = 0.1916 (Rfree = 0.000) for 5183 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 5179 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.98 Search for helices and strands: 0 residues in 0 chains, 5352 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5373 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 11 peptides. Score 0.225 Round 2: 167 peptides, 35 chains. Longest chain 7 peptides. Score 0.246 Round 3: 181 peptides, 37 chains. Longest chain 8 peptides. Score 0.261 Round 4: 193 peptides, 36 chains. Longest chain 11 peptides. Score 0.304 Round 5: 186 peptides, 36 chains. Longest chain 11 peptides. Score 0.286 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vr0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6637 reflections ( 99.51 % complete ) and 12510 restraints for refining 5157 atoms. 11918 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1861 (Rfree = 0.000) for 5157 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1784 (Rfree = 0.000) for 5127 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1949 (Rfree = 0.000) for 5107 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1982 (Rfree = 0.000) for 5085 atoms. TimeTaking 54.42