null Mon 24 Dec 00:22:09 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 2prv-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-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/2prv-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-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 00:22:13 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/2prv-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6591 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 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: 44.420 3.800 Wilson plot Bfac: 83.18 2868 reflections ( 97.72 % complete ) and 0 restraints for refining 2704 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3854 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3376 (Rfree = 0.000) for 2704 atoms. Found 8 (14 requested) and removed 105 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.71 Search for helices and strands: 0 residues in 0 chains, 2640 seeds are put forward NCS extension: 0 residues added, 2640 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.190 Round 2: 79 peptides, 19 chains. Longest chain 5 peptides. Score 0.187 Round 3: 92 peptides, 21 chains. Longest chain 6 peptides. Score 0.218 Round 4: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.310 Round 5: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 5 Chains 20, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5352 restraints for refining 2213 atoms. 5024 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2749 (Rfree = 0.000) for 2213 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.2459 (Rfree = 0.000) for 2191 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2204 (Rfree = 0.000) for 2182 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 2174 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2150 (Rfree = 0.000) for 2171 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.79 Search for helices and strands: 0 residues in 0 chains, 2238 seeds are put forward NCS extension: 0 residues added, 2238 seeds are put forward Round 1: 101 peptides, 23 chains. Longest chain 6 peptides. Score 0.223 Round 2: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.299 Round 3: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.339 Round 4: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.307 Round 5: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.310 Taking the results from Round 3 Chains 20, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5193 restraints for refining 2195 atoms. 4861 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2017 (Rfree = 0.000) for 2195 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.2291 (Rfree = 0.000) for 2183 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2037 (Rfree = 0.000) for 2175 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.1870 (Rfree = 0.000) for 2174 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.1961 (Rfree = 0.000) for 2173 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.68 Search for helices and strands: 0 residues in 0 chains, 2208 seeds are put forward NCS extension: 0 residues added, 2208 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 6 peptides. Score 0.196 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.305 Round 3: 95 peptides, 16 chains. Longest chain 16 peptides. Score 0.363 Round 4: 91 peptides, 16 chains. Longest chain 17 peptides. Score 0.341 Round 5: 90 peptides, 18 chains. Longest chain 11 peptides. Score 0.283 Taking the results from Round 3 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5062 restraints for refining 2160 atoms. 4762 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1963 (Rfree = 0.000) for 2160 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 12: After refmac, R = 0.1974 (Rfree = 0.000) for 2145 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1731 (Rfree = 0.000) for 2142 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 2134 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.1782 (Rfree = 0.000) for 2134 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 2189 seeds are put forward NCS extension: 0 residues added, 2189 seeds are put forward Round 1: 97 peptides, 22 chains. Longest chain 7 peptides. Score 0.224 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.297 Round 3: 117 peptides, 21 chains. Longest chain 9 peptides. Score 0.365 Round 4: 114 peptides, 21 chains. Longest chain 9 peptides. Score 0.348 Round 5: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.350 Taking the results from Round 3 Chains 21, Residues 96, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 4942 restraints for refining 2208 atoms. 4559 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1922 (Rfree = 0.000) for 2208 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.1846 (Rfree = 0.000) for 2203 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.1727 (Rfree = 0.000) for 2195 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.1176 (Rfree = 0.000) for 2195 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1074 (Rfree = 0.000) for 2192 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 2229 seeds are put forward NCS extension: 0 residues added, 2229 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 7 peptides. Score 0.219 Round 2: 94 peptides, 20 chains. Longest chain 8 peptides. Score 0.257 Round 3: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 4: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.294 Round 5: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.311 Taking the results from Round 5 Chains 16, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5135 restraints for refining 2214 atoms. 4871 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1863 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 22: After refmac, R = 0.1710 (Rfree = 0.000) for 2207 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.2000 (Rfree = 0.000) for 2199 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.1571 (Rfree = 0.000) for 2191 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1202 (Rfree = 0.000) for 2191 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.68 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 0 residues added, 2242 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 10 peptides. Score 0.268 Round 2: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.323 Round 3: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.297 Round 4: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.317 Round 5: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Taking the results from Round 2 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 4929 restraints for refining 2172 atoms. 4657 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1577 (Rfree = 0.000) for 2172 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.1543 (Rfree = 0.000) for 2170 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.1120 (Rfree = 0.000) for 2170 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.0885 (Rfree = 0.000) for 2167 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.0881 (Rfree = 0.000) for 2161 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 2209 seeds are put forward NCS extension: 0 residues added, 2209 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.228 Round 2: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.265 Round 3: 71 peptides, 16 chains. Longest chain 5 peptides. Score 0.216 Round 4: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.265 Round 5: 78 peptides, 15 chains. Longest chain 7 peptides. Score 0.289 Taking the results from Round 5 Chains 15, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5045 restraints for refining 2214 atoms. 4808 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1682 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.1767 (Rfree = 0.000) for 2216 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 33: After refmac, R = 0.1825 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.1586 (Rfree = 0.000) for 2211 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.0988 (Rfree = 0.000) for 2215 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 2244 seeds are put forward NCS extension: 0 residues added, 2244 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 6 peptides. Score 0.245 Round 2: 90 peptides, 20 chains. Longest chain 6 peptides. Score 0.232 Round 3: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.300 Round 4: 89 peptides, 18 chains. Longest chain 7 peptides. Score 0.277 Round 5: 88 peptides, 18 chains. Longest chain 7 peptides. Score 0.271 Taking the results from Round 3 Chains 19, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5009 restraints for refining 2214 atoms. 4716 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1540 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.1603 (Rfree = 0.000) for 2207 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.1665 (Rfree = 0.000) for 2208 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.1461 (Rfree = 0.000) for 2202 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.1649 (Rfree = 0.000) for 2200 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2254 seeds are put forward NCS extension: 0 residues added, 2254 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 9 peptides. Score 0.244 Round 2: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.257 Round 3: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 4: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.297 Round 5: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 5 Chains 14, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5184 restraints for refining 2214 atoms. 4934 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 42: After refmac, R = 0.1829 (Rfree = 0.000) for 2202 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.1685 (Rfree = 0.000) for 2203 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1490 (Rfree = 0.000) for 2205 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.1614 (Rfree = 0.000) for 2208 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2267 seeds are put forward NCS extension: 0 residues added, 2267 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.222 Round 2: 73 peptides, 14 chains. Longest chain 7 peptides. Score 0.284 Round 3: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.301 Round 4: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.284 Round 5: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.268 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 65, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2prv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2868 reflections ( 97.72 % complete ) and 5046 restraints for refining 2214 atoms. 4787 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1622 (Rfree = 0.000) for 2214 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1726 (Rfree = 0.000) for 2197 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1623 (Rfree = 0.000) for 2190 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1561 (Rfree = 0.000) for 2183 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:47:36 GMT 2018 Job finished. TimeTaking 25.45 Used memory is bytes: 8140440