Mon 24 Dec 07:46:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr0-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-parrot-noncs ############### 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 07:46:57 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-4.0-parrot-noncs/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-noncs.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-noncs.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 6530 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3409 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3302 (Rfree = 0.000) for 6530 atoms. Found 31 (31 requested) and removed 53 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.98 Search for helices and strands: 0 residues in 0 chains, 6646 seeds are put forward NCS extension: 0 residues added, 6646 seeds are put forward Round 1: 208 peptides, 45 chains. Longest chain 10 peptides. Score 0.244 Round 2: 278 peptides, 51 chains. Longest chain 13 peptides. Score 0.354 Round 3: 322 peptides, 56 chains. Longest chain 13 peptides. Score 0.404 Round 4: 320 peptides, 52 chains. Longest chain 12 peptides. Score 0.437 Round 5: 327 peptides, 48 chains. Longest chain 14 peptides. Score 0.487 Taking the results from Round 5 Chains 48, Residues 279, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12777 restraints for refining 5354 atoms. 11660 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2516 (Rfree = 0.000) for 5354 atoms. Found 17 (25 requested) and removed 48 (12 requested) atoms. Cycle 2: After refmac, R = 0.2532 (Rfree = 0.000) for 5253 atoms. Found 25 (25 requested) and removed 42 (12 requested) atoms. Cycle 3: After refmac, R = 0.2327 (Rfree = 0.000) for 5185 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 4: After refmac, R = 0.2292 (Rfree = 0.000) for 5143 atoms. Found 18 (24 requested) and removed 39 (12 requested) atoms. Cycle 5: After refmac, R = 0.2157 (Rfree = 0.000) for 5101 atoms. Found 19 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 5289 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5306 seeds are put forward Round 1: 295 peptides, 57 chains. Longest chain 10 peptides. Score 0.334 Round 2: 342 peptides, 53 chains. Longest chain 16 peptides. Score 0.473 Round 3: 345 peptides, 51 chains. Longest chain 16 peptides. Score 0.496 Round 4: 366 peptides, 54 chains. Longest chain 15 peptides. Score 0.511 Round 5: 359 peptides, 52 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 5 Chains 54, Residues 307, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12367 restraints for refining 5248 atoms. 11158 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2147 (Rfree = 0.000) for 5248 atoms. Found 12 (24 requested) and removed 54 (12 requested) atoms. Cycle 7: After refmac, R = 0.2122 (Rfree = 0.000) for 5170 atoms. Found 14 (24 requested) and removed 40 (12 requested) atoms. Cycle 8: After refmac, R = 0.2036 (Rfree = 0.000) for 5126 atoms. Found 13 (24 requested) and removed 35 (12 requested) atoms. Cycle 9: After refmac, R = 0.2068 (Rfree = 0.000) for 5086 atoms. Found 18 (24 requested) and removed 29 (12 requested) atoms. Cycle 10: After refmac, R = 0.1803 (Rfree = 0.000) for 5061 atoms. Found 12 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.97 Search for helices and strands: 0 residues in 0 chains, 5262 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5279 seeds are put forward Round 1: 279 peptides, 51 chains. Longest chain 10 peptides. Score 0.356 Round 2: 314 peptides, 50 chains. Longest chain 17 peptides. Score 0.442 Round 3: 307 peptides, 48 chains. Longest chain 17 peptides. Score 0.446 Round 4: 327 peptides, 49 chains. Longest chain 19 peptides. Score 0.478 Round 5: 332 peptides, 47 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 5 Chains 47, Residues 285, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12637 restraints for refining 5340 atoms. 11544 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 5340 atoms. Found 21 (25 requested) and removed 61 (12 requested) atoms. Cycle 12: After refmac, R = 0.2188 (Rfree = 0.000) for 5270 atoms. Found 25 (25 requested) and removed 50 (12 requested) atoms. Cycle 13: After refmac, R = 0.1956 (Rfree = 0.000) for 5228 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 14: After refmac, R = 0.1490 (Rfree = 0.000) for 5210 atoms. Found 3 (24 requested) and removed 21 (12 requested) atoms. Cycle 15: After refmac, R = 0.1410 (Rfree = 0.000) for 5181 atoms. Found 2 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.99 Search for helices and strands: 0 residues in 0 chains, 5323 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5342 seeds are put forward Round 1: 290 peptides, 60 chains. Longest chain 10 peptides. Score 0.293 Round 2: 317 peptides, 55 chains. Longest chain 17 peptides. Score 0.403 Round 3: 315 peptides, 50 chains. Longest chain 16 peptides. Score 0.444 Round 4: 308 peptides, 49 chains. Longest chain 20 peptides. Score 0.439 Round 5: 336 peptides, 54 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 5 Chains 54, Residues 282, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12755 restraints for refining 5353 atoms. 11681 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2241 (Rfree = 0.000) for 5353 atoms. Found 21 (25 requested) and removed 50 (12 requested) atoms. Cycle 17: After refmac, R = 0.2094 (Rfree = 0.000) for 5290 atoms. Found 20 (25 requested) and removed 36 (12 requested) atoms. Cycle 18: After refmac, R = 0.2144 (Rfree = 0.000) for 5258 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 19: After refmac, R = 0.1926 (Rfree = 0.000) for 5229 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 20: After refmac, R = 0.1989 (Rfree = 0.000) for 5214 atoms. Found 22 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.92 Search for helices and strands: 0 residues in 0 chains, 5395 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5420 seeds are put forward Round 1: 255 peptides, 51 chains. Longest chain 10 peptides. Score 0.299 Round 2: 303 peptides, 51 chains. Longest chain 15 peptides. Score 0.410 Round 3: 285 peptides, 49 chains. Longest chain 13 peptides. Score 0.389 Round 4: 294 peptides, 47 chains. Longest chain 13 peptides. Score 0.428 Round 5: 295 peptides, 48 chains. Longest chain 21 peptides. Score 0.421 Taking the results from Round 4 Chains 47, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 13020 restraints for refining 5352 atoms. 12079 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1998 (Rfree = 0.000) for 5352 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 22: After refmac, R = 0.2150 (Rfree = 0.000) for 5315 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 23: After refmac, R = 0.2148 (Rfree = 0.000) for 5283 atoms. Found 21 (25 requested) and removed 29 (12 requested) atoms. Cycle 24: After refmac, R = 0.2112 (Rfree = 0.000) for 5254 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 25: After refmac, R = 0.1961 (Rfree = 0.000) for 5228 atoms. Found 18 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 4.00 Search for helices and strands: 0 residues in 0 chains, 5420 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5434 seeds are put forward Round 1: 240 peptides, 50 chains. Longest chain 12 peptides. Score 0.272 Round 2: 280 peptides, 49 chains. Longest chain 10 peptides. Score 0.378 Round 3: 277 peptides, 48 chains. Longest chain 12 peptides. Score 0.381 Round 4: 307 peptides, 51 chains. Longest chain 15 peptides. Score 0.418 Round 5: 289 peptides, 45 chains. Longest chain 17 peptides. Score 0.436 Taking the results from Round 5 Chains 45, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12941 restraints for refining 5353 atoms. 12010 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2134 (Rfree = 0.000) for 5353 atoms. Found 15 (25 requested) and removed 30 (12 requested) atoms. Cycle 27: After refmac, R = 0.2082 (Rfree = 0.000) for 5309 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 28: After refmac, R = 0.2104 (Rfree = 0.000) for 5288 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 29: After refmac, R = 0.2019 (Rfree = 0.000) for 5273 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 30: After refmac, R = 0.2123 (Rfree = 0.000) for 5244 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.97 Search for helices and strands: 0 residues in 0 chains, 5409 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5433 seeds are put forward Round 1: 224 peptides, 51 chains. Longest chain 8 peptides. Score 0.221 Round 2: 243 peptides, 47 chains. Longest chain 14 peptides. Score 0.311 Round 3: 247 peptides, 43 chains. Longest chain 13 peptides. Score 0.362 Round 4: 254 peptides, 45 chains. Longest chain 15 peptides. Score 0.358 Round 5: 258 peptides, 43 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 5 Chains 43, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12754 restraints for refining 5313 atoms. 11937 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2189 (Rfree = 0.000) for 5313 atoms. Found 25 (25 requested) and removed 52 (12 requested) atoms. Cycle 32: After refmac, R = 0.2093 (Rfree = 0.000) for 5267 atoms. Found 25 (25 requested) and removed 36 (12 requested) atoms. Cycle 33: After refmac, R = 0.2076 (Rfree = 0.000) for 5237 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 34: After refmac, R = 0.1440 (Rfree = 0.000) for 5220 atoms. Found 5 (24 requested) and removed 18 (12 requested) atoms. Cycle 35: After refmac, R = 0.1365 (Rfree = 0.000) for 5200 atoms. Found 2 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 5326 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5340 seeds are put forward Round 1: 212 peptides, 44 chains. Longest chain 10 peptides. Score 0.265 Round 2: 241 peptides, 45 chains. Longest chain 11 peptides. Score 0.327 Round 3: 261 peptides, 46 chains. Longest chain 11 peptides. Score 0.364 Round 4: 260 peptides, 45 chains. Longest chain 12 peptides. Score 0.372 Round 5: 254 peptides, 43 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 5 Chains 43, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12833 restraints for refining 5333 atoms. 12032 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2055 (Rfree = 0.000) for 5333 atoms. Found 25 (25 requested) and removed 47 (12 requested) atoms. Cycle 37: After refmac, R = 0.1996 (Rfree = 0.000) for 5281 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1967 (Rfree = 0.000) for 5256 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. Cycle 39: After refmac, R = 0.2123 (Rfree = 0.000) for 5238 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 40: After refmac, R = 0.2200 (Rfree = 0.000) for 5218 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.93 Search for helices and strands: 0 residues in 0 chains, 5370 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5383 seeds are put forward Round 1: 158 peptides, 35 chains. Longest chain 7 peptides. Score 0.221 Round 2: 176 peptides, 37 chains. Longest chain 8 peptides. Score 0.248 Round 3: 193 peptides, 37 chains. Longest chain 9 peptides. Score 0.293 Round 4: 217 peptides, 39 chains. Longest chain 9 peptides. Score 0.332 Round 5: 212 peptides, 37 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 5 Chains 37, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6637 reflections ( 99.51 % complete ) and 12368 restraints for refining 5167 atoms. 11705 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2223 (Rfree = 0.000) for 5167 atoms. Found 24 (24 requested) and removed 45 (12 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 5134 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 43: After refmac, R = 0.2194 (Rfree = 0.000) for 5121 atoms. Found 24 (24 requested) and removed 53 (12 requested) atoms. Cycle 44: After refmac, R = 0.1898 (Rfree = 0.000) for 5081 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 45: After refmac, R = 0.2032 (Rfree = 0.000) for 5073 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.92 Search for helices and strands: 0 residues in 0 chains, 5212 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 5222 seeds are put forward Round 1: 146 peptides, 32 chains. Longest chain 7 peptides. Score 0.222 Round 2: 185 peptides, 36 chains. Longest chain 10 peptides. Score 0.283 Round 3: 180 peptides, 34 chains. Longest chain 8 peptides. Score 0.293 Round 4: 200 peptides, 36 chains. Longest chain 10 peptides. Score 0.322 Round 5: 193 peptides, 34 chains. Longest chain 14 peptides. Score 0.327 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 159, 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 11983 restraints for refining 4995 atoms. 11381 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1947 (Rfree = 0.000) for 4995 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2103 (Rfree = 0.000) for 4970 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1926 (Rfree = 0.000) for 4946 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2082 (Rfree = 0.000) for 4918 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 54.23