Mon 24 Dec 08:00:15 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 2op5-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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/2op5-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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 08:00:20 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/2op5-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.6-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 484 and 0 Target number of residues in the AU: 484 Target solvent content: 0.6225 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.6-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 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: 73.087 3.600 Wilson plot Bfac: 62.34 8519 reflections ( 99.80 % complete ) and 0 restraints for refining 6194 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3410 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3084 (Rfree = 0.000) for 6194 atoms. Found 32 (39 requested) and removed 71 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 6270 seeds are put forward NCS extension: 0 residues added, 6270 seeds are put forward Round 1: 214 peptides, 44 chains. Longest chain 13 peptides. Score 0.274 Round 2: 295 peptides, 59 chains. Longest chain 12 peptides. Score 0.321 Round 3: 320 peptides, 57 chains. Longest chain 19 peptides. Score 0.400 Round 4: 326 peptides, 55 chains. Longest chain 19 peptides. Score 0.432 Round 5: 330 peptides, 54 chains. Longest chain 21 peptides. Score 0.451 Taking the results from Round 5 Chains 54, Residues 276, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11915 restraints for refining 5089 atoms. 10865 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2478 (Rfree = 0.000) for 5089 atoms. Found 20 (32 requested) and removed 38 (16 requested) atoms. Cycle 2: After refmac, R = 0.2212 (Rfree = 0.000) for 5023 atoms. Found 8 (32 requested) and removed 31 (16 requested) atoms. Cycle 3: After refmac, R = 0.2176 (Rfree = 0.000) for 4975 atoms. Found 11 (32 requested) and removed 33 (16 requested) atoms. Cycle 4: After refmac, R = 0.1910 (Rfree = 0.000) for 4932 atoms. Found 7 (31 requested) and removed 16 (15 requested) atoms. Cycle 5: After refmac, R = 0.1906 (Rfree = 0.000) for 4915 atoms. Found 3 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 5067 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 5090 seeds are put forward Round 1: 243 peptides, 47 chains. Longest chain 10 peptides. Score 0.317 Round 2: 273 peptides, 47 chains. Longest chain 10 peptides. Score 0.390 Round 3: 286 peptides, 50 chains. Longest chain 16 peptides. Score 0.390 Round 4: 282 peptides, 47 chains. Longest chain 17 peptides. Score 0.411 Round 5: 305 peptides, 47 chains. Longest chain 17 peptides. Score 0.462 Taking the results from Round 5 Chains 47, Residues 258, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11905 restraints for refining 5038 atoms. 10920 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2174 (Rfree = 0.000) for 5038 atoms. Found 16 (32 requested) and removed 44 (16 requested) atoms. Cycle 7: After refmac, R = 0.2185 (Rfree = 0.000) for 4983 atoms. Found 16 (32 requested) and removed 30 (16 requested) atoms. Cycle 8: After refmac, R = 0.2162 (Rfree = 0.000) for 4947 atoms. Found 14 (31 requested) and removed 28 (15 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 4917 atoms. Found 21 (31 requested) and removed 26 (15 requested) atoms. Cycle 10: After refmac, R = 0.2203 (Rfree = 0.000) for 4906 atoms. Found 22 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5049 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5062 seeds are put forward Round 1: 233 peptides, 45 chains. Longest chain 11 peptides. Score 0.313 Round 2: 292 peptides, 52 chains. Longest chain 15 peptides. Score 0.384 Round 3: 294 peptides, 48 chains. Longest chain 15 peptides. Score 0.429 Round 4: 287 peptides, 49 chains. Longest chain 15 peptides. Score 0.403 Round 5: 307 peptides, 45 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 5 Chains 45, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11635 restraints for refining 5015 atoms. 10632 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2154 (Rfree = 0.000) for 5015 atoms. Found 17 (32 requested) and removed 60 (16 requested) atoms. Cycle 12: After refmac, R = 0.1950 (Rfree = 0.000) for 4951 atoms. Found 16 (31 requested) and removed 31 (15 requested) atoms. Cycle 13: After refmac, R = 0.1628 (Rfree = 0.000) for 4925 atoms. Found 5 (31 requested) and removed 18 (15 requested) atoms. Cycle 14: After refmac, R = 0.1702 (Rfree = 0.000) for 4908 atoms. Found 5 (31 requested) and removed 19 (15 requested) atoms. Cycle 15: After refmac, R = 0.1858 (Rfree = 0.000) for 4893 atoms. Found 11 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 5043 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5068 seeds are put forward Round 1: 244 peptides, 47 chains. Longest chain 11 peptides. Score 0.320 Round 2: 285 peptides, 46 chains. Longest chain 12 peptides. Score 0.428 Round 3: 304 peptides, 48 chains. Longest chain 20 peptides. Score 0.451 Round 4: 297 peptides, 48 chains. Longest chain 18 peptides. Score 0.435 Round 5: 295 peptides, 48 chains. Longest chain 17 peptides. Score 0.431 Taking the results from Round 3 Chains 48, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11813 restraints for refining 5091 atoms. 10837 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2051 (Rfree = 0.000) for 5091 atoms. Found 14 (32 requested) and removed 39 (16 requested) atoms. Cycle 17: After refmac, R = 0.1996 (Rfree = 0.000) for 5051 atoms. Found 11 (32 requested) and removed 24 (16 requested) atoms. Cycle 18: After refmac, R = 0.1922 (Rfree = 0.000) for 5027 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. Cycle 19: After refmac, R = 0.1914 (Rfree = 0.000) for 5009 atoms. Found 13 (32 requested) and removed 27 (16 requested) atoms. Cycle 20: After refmac, R = 0.1848 (Rfree = 0.000) for 4991 atoms. Found 3 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 5122 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 5148 seeds are put forward Round 1: 254 peptides, 51 chains. Longest chain 11 peptides. Score 0.302 Round 2: 275 peptides, 46 chains. Longest chain 15 peptides. Score 0.405 Round 3: 276 peptides, 46 chains. Longest chain 15 peptides. Score 0.407 Round 4: 281 peptides, 43 chains. Longest chain 16 peptides. Score 0.448 Round 5: 291 peptides, 47 chains. Longest chain 18 peptides. Score 0.432 Taking the results from Round 4 Chains 43, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11818 restraints for refining 5091 atoms. 10909 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2147 (Rfree = 0.000) for 5091 atoms. Found 16 (32 requested) and removed 25 (16 requested) atoms. Cycle 22: After refmac, R = 0.1933 (Rfree = 0.000) for 5069 atoms. Found 15 (32 requested) and removed 20 (16 requested) atoms. Cycle 23: After refmac, R = 0.1846 (Rfree = 0.000) for 5056 atoms. Found 5 (32 requested) and removed 17 (16 requested) atoms. Cycle 24: After refmac, R = 0.1837 (Rfree = 0.000) for 5036 atoms. Found 10 (32 requested) and removed 22 (16 requested) atoms. Cycle 25: After refmac, R = 0.1856 (Rfree = 0.000) for 5021 atoms. Found 6 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 5153 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5173 seeds are put forward Round 1: 215 peptides, 45 chains. Longest chain 10 peptides. Score 0.266 Round 2: 241 peptides, 46 chains. Longest chain 12 peptides. Score 0.323 Round 3: 248 peptides, 43 chains. Longest chain 14 peptides. Score 0.372 Round 4: 276 peptides, 45 chains. Longest chain 15 peptides. Score 0.417 Round 5: 262 peptides, 45 chains. Longest chain 14 peptides. Score 0.385 Taking the results from Round 4 Chains 45, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12074 restraints for refining 5091 atoms. 11195 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2089 (Rfree = 0.000) for 5091 atoms. Found 21 (32 requested) and removed 35 (16 requested) atoms. Cycle 27: After refmac, R = 0.1925 (Rfree = 0.000) for 5067 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. Cycle 28: After refmac, R = 0.1988 (Rfree = 0.000) for 5045 atoms. Found 6 (32 requested) and removed 23 (16 requested) atoms. Cycle 29: After refmac, R = 0.2031 (Rfree = 0.000) for 5023 atoms. Found 14 (32 requested) and removed 34 (16 requested) atoms. Cycle 30: After refmac, R = 0.1744 (Rfree = 0.000) for 5001 atoms. Found 7 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 5130 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5149 seeds are put forward Round 1: 224 peptides, 46 chains. Longest chain 11 peptides. Score 0.279 Round 2: 233 peptides, 42 chains. Longest chain 14 peptides. Score 0.346 Round 3: 249 peptides, 44 chains. Longest chain 22 peptides. Score 0.364 Round 4: 257 peptides, 47 chains. Longest chain 17 peptides. Score 0.352 Round 5: 267 peptides, 45 chains. Longest chain 18 peptides. Score 0.397 Taking the results from Round 5 Chains 45, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 11958 restraints for refining 5091 atoms. 11115 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2029 (Rfree = 0.000) for 5091 atoms. Found 10 (32 requested) and removed 37 (16 requested) atoms. Cycle 32: After refmac, R = 0.1973 (Rfree = 0.000) for 5050 atoms. Found 11 (32 requested) and removed 23 (16 requested) atoms. Cycle 33: After refmac, R = 0.1930 (Rfree = 0.000) for 5030 atoms. Found 11 (32 requested) and removed 19 (16 requested) atoms. Cycle 34: After refmac, R = 0.1661 (Rfree = 0.000) for 5018 atoms. Found 5 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.1664 (Rfree = 0.000) for 5001 atoms. Found 4 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 5106 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5123 seeds are put forward Round 1: 231 peptides, 47 chains. Longest chain 11 peptides. Score 0.286 Round 2: 224 peptides, 38 chains. Longest chain 15 peptides. Score 0.367 Round 3: 233 peptides, 43 chains. Longest chain 17 peptides. Score 0.335 Round 4: 238 peptides, 41 chains. Longest chain 16 peptides. Score 0.369 Round 5: 239 peptides, 40 chains. Longest chain 19 peptides. Score 0.382 Taking the results from Round 5 Chains 40, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12128 restraints for refining 5090 atoms. 11372 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1896 (Rfree = 0.000) for 5090 atoms. Found 7 (32 requested) and removed 30 (16 requested) atoms. Cycle 37: After refmac, R = 0.1857 (Rfree = 0.000) for 5051 atoms. Found 14 (32 requested) and removed 27 (16 requested) atoms. Cycle 38: After refmac, R = 0.1865 (Rfree = 0.000) for 5033 atoms. Found 12 (32 requested) and removed 24 (16 requested) atoms. Cycle 39: After refmac, R = 0.1872 (Rfree = 0.000) for 5017 atoms. Found 17 (32 requested) and removed 21 (16 requested) atoms. Cycle 40: After refmac, R = 0.1516 (Rfree = 0.000) for 5007 atoms. Found 4 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 5121 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 5155 seeds are put forward Round 1: 204 peptides, 44 chains. Longest chain 11 peptides. Score 0.247 Round 2: 225 peptides, 44 chains. Longest chain 11 peptides. Score 0.303 Round 3: 219 peptides, 43 chains. Longest chain 10 peptides. Score 0.299 Round 4: 219 peptides, 44 chains. Longest chain 10 peptides. Score 0.288 Round 5: 209 peptides, 39 chains. Longest chain 15 peptides. Score 0.318 Taking the results from Round 5 Chains 39, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8519 reflections ( 99.80 % complete ) and 12117 restraints for refining 5079 atoms. 11476 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 5079 atoms. Found 9 (32 requested) and removed 32 (16 requested) atoms. Cycle 42: After refmac, R = 0.2024 (Rfree = 0.000) for 5047 atoms. Found 28 (32 requested) and removed 21 (16 requested) atoms. Cycle 43: After refmac, R = 0.1857 (Rfree = 0.000) for 5044 atoms. Found 5 (32 requested) and removed 28 (16 requested) atoms. Cycle 44: After refmac, R = 0.1583 (Rfree = 0.000) for 5017 atoms. Found 3 (32 requested) and removed 18 (16 requested) atoms. Cycle 45: After refmac, R = 0.1549 (Rfree = 0.000) for 5000 atoms. Found 5 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5165 seeds are put forward Round 1: 175 peptides, 37 chains. Longest chain 10 peptides. Score 0.248 Round 2: 193 peptides, 36 chains. Longest chain 9 peptides. Score 0.309 Round 3: 195 peptides, 38 chains. Longest chain 12 peptides. Score 0.292 Round 4: 197 peptides, 35 chains. Longest chain 12 peptides. Score 0.332 Round 5: 179 peptides, 33 chains. Longest chain 12 peptides. Score 0.307 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 162, 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 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8519 reflections ( 99.80 % complete ) and 12303 restraints for refining 5091 atoms. 11690 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1910 (Rfree = 0.000) for 5091 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1867 (Rfree = 0.000) for 5063 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1887 (Rfree = 0.000) for 5038 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1795 (Rfree = 0.000) for 5019 atoms. TimeTaking 51.58