Mon 24 Dec 08:07:46 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 2eth-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-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/2eth-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-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 08:07:50 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/2eth-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6563 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.56 Input MTZ file: 2eth-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 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: 65.143 3.600 Wilson plot Bfac: 82.21 4336 reflections ( 98.17 % complete ) and 0 restraints for refining 2717 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3433 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3295 (Rfree = 0.000) for 2717 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 2782 seeds are put forward NCS extension: 0 residues added, 2782 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 7 peptides. Score 0.291 Round 2: 145 peptides, 23 chains. Longest chain 11 peptides. Score 0.424 Round 3: 161 peptides, 21 chains. Longest chain 13 peptides. Score 0.522 Round 4: 157 peptides, 21 chains. Longest chain 13 peptides. Score 0.507 Round 5: 152 peptides, 21 chains. Longest chain 13 peptides. Score 0.488 Taking the results from Round 3 Chains 21, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5320 restraints for refining 2231 atoms. 4781 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2539 (Rfree = 0.000) for 2231 atoms. Found 13 (14 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2418 (Rfree = 0.000) for 2198 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 3: After refmac, R = 0.2415 (Rfree = 0.000) for 2188 atoms. Found 9 (14 requested) and removed 18 (7 requested) atoms. Cycle 4: After refmac, R = 0.2420 (Rfree = 0.000) for 2173 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2363 (Rfree = 0.000) for 2175 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 2272 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2283 seeds are put forward Round 1: 144 peptides, 23 chains. Longest chain 10 peptides. Score 0.419 Round 2: 157 peptides, 23 chains. Longest chain 22 peptides. Score 0.472 Round 3: 143 peptides, 19 chains. Longest chain 16 peptides. Score 0.488 Round 4: 156 peptides, 21 chains. Longest chain 24 peptides. Score 0.503 Round 5: 160 peptides, 20 chains. Longest chain 16 peptides. Score 0.535 Taking the results from Round 5 Chains 20, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5319 restraints for refining 2233 atoms. 4779 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2413 (Rfree = 0.000) for 2233 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 7: After refmac, R = 0.2244 (Rfree = 0.000) for 2214 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2256 (Rfree = 0.000) for 2200 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.2207 (Rfree = 0.000) for 2191 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.1988 (Rfree = 0.000) for 2184 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2299 seeds are put forward Round 1: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.404 Round 2: 144 peptides, 21 chains. Longest chain 17 peptides. Score 0.456 Round 3: 154 peptides, 22 chains. Longest chain 14 peptides. Score 0.478 Round 4: 152 peptides, 21 chains. Longest chain 13 peptides. Score 0.488 Round 5: 153 peptides, 19 chains. Longest chain 17 peptides. Score 0.526 Taking the results from Round 5 Chains 19, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5303 restraints for refining 2232 atoms. 4786 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2274 (Rfree = 0.000) for 2232 atoms. Found 4 (14 requested) and removed 17 (7 requested) atoms. Cycle 12: After refmac, R = 0.2163 (Rfree = 0.000) for 2212 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2142 (Rfree = 0.000) for 2200 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.2149 (Rfree = 0.000) for 2192 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.2243 (Rfree = 0.000) for 2190 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2285 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2301 seeds are put forward Round 1: 146 peptides, 23 chains. Longest chain 12 peptides. Score 0.428 Round 2: 158 peptides, 21 chains. Longest chain 19 peptides. Score 0.511 Round 3: 160 peptides, 24 chains. Longest chain 14 peptides. Score 0.467 Round 4: 157 peptides, 24 chains. Longest chain 15 peptides. Score 0.455 Round 5: 162 peptides, 20 chains. Longest chain 16 peptides. Score 0.542 Taking the results from Round 5 Chains 20, Residues 142, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5052 restraints for refining 2233 atoms. 4454 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2416 (Rfree = 0.000) for 2233 atoms. Found 11 (14 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.2197 (Rfree = 0.000) for 2219 atoms. Found 1 (14 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.2097 (Rfree = 0.000) for 2201 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2076 (Rfree = 0.000) for 2188 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2016 (Rfree = 0.000) for 2182 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 2302 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2318 seeds are put forward Round 1: 134 peptides, 23 chains. Longest chain 15 peptides. Score 0.376 Round 2: 160 peptides, 24 chains. Longest chain 13 peptides. Score 0.467 Round 3: 151 peptides, 24 chains. Longest chain 12 peptides. Score 0.430 Round 4: 159 peptides, 20 chains. Longest chain 14 peptides. Score 0.532 Round 5: 154 peptides, 22 chains. Longest chain 17 peptides. Score 0.478 Taking the results from Round 4 Chains 20, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5131 restraints for refining 2231 atoms. 4595 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2310 (Rfree = 0.000) for 2231 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 22: After refmac, R = 0.2175 (Rfree = 0.000) for 2218 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 23: After refmac, R = 0.2126 (Rfree = 0.000) for 2214 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.2115 (Rfree = 0.000) for 2209 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2105 (Rfree = 0.000) for 2201 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2298 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2316 seeds are put forward Round 1: 147 peptides, 24 chains. Longest chain 13 peptides. Score 0.413 Round 2: 148 peptides, 23 chains. Longest chain 17 peptides. Score 0.436 Round 3: 144 peptides, 24 chains. Longest chain 9 peptides. Score 0.401 Round 4: 152 peptides, 25 chains. Longest chain 17 peptides. Score 0.416 Round 5: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 2 Chains 23, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5259 restraints for refining 2231 atoms. 4782 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 2231 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2123 (Rfree = 0.000) for 2217 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.2070 (Rfree = 0.000) for 2212 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2069 (Rfree = 0.000) for 2204 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2059 (Rfree = 0.000) for 2198 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 2276 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 10 peptides. Score 0.369 Round 2: 145 peptides, 24 chains. Longest chain 15 peptides. Score 0.405 Round 3: 132 peptides, 20 chains. Longest chain 17 peptides. Score 0.425 Round 4: 137 peptides, 20 chains. Longest chain 13 peptides. Score 0.446 Round 5: 136 peptides, 21 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 4 Chains 20, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5274 restraints for refining 2233 atoms. 4826 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2351 (Rfree = 0.000) for 2233 atoms. Found 12 (14 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.2143 (Rfree = 0.000) for 2227 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.2084 (Rfree = 0.000) for 2221 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.2078 (Rfree = 0.000) for 2214 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2054 (Rfree = 0.000) for 2208 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2260 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.280 Round 2: 123 peptides, 22 chains. Longest chain 13 peptides. Score 0.346 Round 3: 121 peptides, 20 chains. Longest chain 12 peptides. Score 0.377 Round 4: 138 peptides, 21 chains. Longest chain 15 peptides. Score 0.431 Round 5: 135 peptides, 20 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 5 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5315 restraints for refining 2233 atoms. 4875 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2382 (Rfree = 0.000) for 2233 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.2467 (Rfree = 0.000) for 2224 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2346 (Rfree = 0.000) for 2218 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.2118 (Rfree = 0.000) for 2216 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.2026 (Rfree = 0.000) for 2210 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2295 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.242 Round 2: 106 peptides, 18 chains. Longest chain 13 peptides. Score 0.348 Round 3: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.314 Round 4: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.325 Round 5: 110 peptides, 19 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 2 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5503 restraints for refining 2232 atoms. 5169 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2162 (Rfree = 0.000) for 2232 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.2089 (Rfree = 0.000) for 2229 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1947 (Rfree = 0.000) for 2222 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1891 (Rfree = 0.000) for 2213 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1922 (Rfree = 0.000) for 2205 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward NCS extension: 0 residues added, 2274 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 9 peptides. Score 0.236 Round 2: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.286 Round 3: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.360 Round 4: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.355 Round 5: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.353 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 94, 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 2eth-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4336 reflections ( 98.17 % complete ) and 5428 restraints for refining 2233 atoms. 5071 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2156 (Rfree = 0.000) for 2233 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2301 (Rfree = 0.000) for 2218 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2247 (Rfree = 0.000) for 2208 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2343 (Rfree = 0.000) for 2200 atoms. TimeTaking 30.47