Mon 24 Dec 00:47:37 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 2eth-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-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/2eth-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-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 00:47:41 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/2eth-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-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 235 and 0 Target number of residues in the AU: 235 Target solvent content: 0.6620 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-3.8-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 85.72 3696 reflections ( 98.14 % complete ) and 0 restraints for refining 2724 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3382 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3281 (Rfree = 0.000) for 2724 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.44 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: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.307 Round 2: 129 peptides, 19 chains. Longest chain 14 peptides. Score 0.431 Round 3: 134 peptides, 18 chains. Longest chain 12 peptides. Score 0.471 Round 4: 152 peptides, 22 chains. Longest chain 15 peptides. Score 0.470 Round 5: 144 peptides, 20 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 5 Chains 20, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5147 restraints for refining 2153 atoms. 4671 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2567 (Rfree = 0.000) for 2153 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.2496 (Rfree = 0.000) for 2117 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2477 (Rfree = 0.000) for 2086 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2463 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2394 (Rfree = 0.000) for 2051 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2162 seeds are put forward Round 1: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.395 Round 2: 133 peptides, 19 chains. Longest chain 12 peptides. Score 0.448 Round 3: 143 peptides, 18 chains. Longest chain 15 peptides. Score 0.506 Round 4: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.474 Round 5: 143 peptides, 18 chains. Longest chain 16 peptides. Score 0.506 Taking the results from Round 5 Chains 18, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4456 restraints for refining 1985 atoms. 3974 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2326 (Rfree = 0.000) for 1985 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.2231 (Rfree = 0.000) for 1968 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2250 (Rfree = 0.000) for 1956 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2241 (Rfree = 0.000) for 1948 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2285 (Rfree = 0.000) for 1943 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 3.52 Search for helices and strands: 0 residues in 0 chains, 2046 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2057 seeds are put forward Round 1: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.396 Round 2: 144 peptides, 17 chains. Longest chain 22 peptides. Score 0.527 Round 3: 148 peptides, 19 chains. Longest chain 17 peptides. Score 0.508 Round 4: 138 peptides, 19 chains. Longest chain 20 peptides. Score 0.468 Round 5: 159 peptides, 20 chains. Longest chain 21 peptides. Score 0.532 Taking the results from Round 5 Chains 20, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4560 restraints for refining 2052 atoms. 4024 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2225 (Rfree = 0.000) for 2052 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2159 (Rfree = 0.000) for 2033 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2013 (Rfree = 0.000) for 2024 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.2025 (Rfree = 0.000) for 2019 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2126 (Rfree = 0.000) for 2015 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.44 Search for helices and strands: 0 residues in 0 chains, 2112 seeds are put forward NCS extension: 0 residues added, 2112 seeds are put forward Round 1: 134 peptides, 22 chains. Longest chain 14 peptides. Score 0.395 Round 2: 141 peptides, 21 chains. Longest chain 14 peptides. Score 0.444 Round 3: 141 peptides, 20 chains. Longest chain 15 peptides. Score 0.462 Round 4: 151 peptides, 20 chains. Longest chain 17 peptides. Score 0.502 Round 5: 139 peptides, 19 chains. Longest chain 14 peptides. Score 0.472 Taking the results from Round 4 Chains 20, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 4689 restraints for refining 2140 atoms. 4185 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2089 (Rfree = 0.000) for 2140 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 17: After refmac, R = 0.2108 (Rfree = 0.000) for 2118 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2165 (Rfree = 0.000) for 2111 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.1958 (Rfree = 0.000) for 2105 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.2083 (Rfree = 0.000) for 2092 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.48 Search for helices and strands: 0 residues in 0 chains, 2199 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2220 seeds are put forward Round 1: 122 peptides, 22 chains. Longest chain 10 peptides. Score 0.341 Round 2: 143 peptides, 22 chains. Longest chain 12 peptides. Score 0.434 Round 3: 144 peptides, 20 chains. Longest chain 14 peptides. Score 0.474 Round 4: 137 peptides, 17 chains. Longest chain 16 peptides. Score 0.501 Round 5: 141 peptides, 20 chains. Longest chain 11 peptides. Score 0.462 Taking the results from Round 4 Chains 17, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5020 restraints for refining 2189 atoms. 4557 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2306 (Rfree = 0.000) for 2189 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 22: After refmac, R = 0.2110 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 23: After refmac, R = 0.2031 (Rfree = 0.000) for 2141 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 24: After refmac, R = 0.2115 (Rfree = 0.000) for 2130 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.2022 (Rfree = 0.000) for 2119 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.47 Search for helices and strands: 0 residues in 0 chains, 2195 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2213 seeds are put forward Round 1: 116 peptides, 23 chains. Longest chain 12 peptides. Score 0.292 Round 2: 134 peptides, 23 chains. Longest chain 13 peptides. Score 0.376 Round 3: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.356 Round 4: 141 peptides, 22 chains. Longest chain 13 peptides. Score 0.425 Round 5: 140 peptides, 21 chains. Longest chain 12 peptides. Score 0.440 Taking the results from Round 5 Chains 21, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5130 restraints for refining 2216 atoms. 4675 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2097 (Rfree = 0.000) for 2216 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2109 (Rfree = 0.000) for 2206 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.2128 (Rfree = 0.000) for 2204 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.2062 (Rfree = 0.000) for 2193 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1998 (Rfree = 0.000) for 2181 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 2270 seeds are put forward NCS extension: 0 residues added, 2270 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 7 peptides. Score 0.258 Round 2: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.340 Round 3: 118 peptides, 17 chains. Longest chain 13 peptides. Score 0.423 Round 4: 120 peptides, 21 chains. Longest chain 11 peptides. Score 0.352 Round 5: 135 peptides, 22 chains. Longest chain 15 peptides. Score 0.400 Taking the results from Round 3 Chains 17, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5187 restraints for refining 2229 atoms. 4800 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2070 (Rfree = 0.000) for 2229 atoms. Found 8 (12 requested) and removed 20 (6 requested) atoms. Cycle 32: After refmac, R = 0.2025 (Rfree = 0.000) for 2199 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 33: After refmac, R = 0.2093 (Rfree = 0.000) for 2188 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.1926 (Rfree = 0.000) for 2182 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 35: After refmac, R = 0.1937 (Rfree = 0.000) for 2176 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.40 Search for helices and strands: 0 residues in 0 chains, 2255 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2273 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.299 Round 2: 113 peptides, 19 chains. Longest chain 20 peptides. Score 0.360 Round 3: 114 peptides, 20 chains. Longest chain 10 peptides. Score 0.344 Round 4: 108 peptides, 19 chains. Longest chain 9 peptides. Score 0.337 Round 5: 114 peptides, 21 chains. Longest chain 11 peptides. Score 0.324 Taking the results from Round 2 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5071 restraints for refining 2196 atoms. 4714 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1981 (Rfree = 0.000) for 2196 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.1972 (Rfree = 0.000) for 2190 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2041 (Rfree = 0.000) for 2184 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1853 (Rfree = 0.000) for 2175 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.2145 (Rfree = 0.000) for 2168 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 2258 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2279 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 8 peptides. Score 0.237 Round 2: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.363 Round 3: 121 peptides, 21 chains. Longest chain 13 peptides. Score 0.357 Round 4: 119 peptides, 21 chains. Longest chain 8 peptides. Score 0.347 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 5 Chains 20, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3696 reflections ( 98.14 % complete ) and 5143 restraints for refining 2228 atoms. 4771 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2085 (Rfree = 0.000) for 2228 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2107 (Rfree = 0.000) for 2213 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1999 (Rfree = 0.000) for 2209 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1911 (Rfree = 0.000) for 2207 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 2203 atoms. Found 9 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 2324 seeds are put forward NCS extension: 0 residues added, 2324 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 7 peptides. Score 0.231 Round 2: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.273 Round 3: 101 peptides, 19 chains. Longest chain 13 peptides. Score 0.303 Round 4: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.320 Round 5: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 89, 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. 3696 reflections ( 98.14 % complete ) and 5147 restraints for refining 2210 atoms. 4811 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2047 (Rfree = 0.000) for 2210 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2117 (Rfree = 0.000) for 2198 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2034 (Rfree = 0.000) for 2187 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2042 (Rfree = 0.000) for 2177 atoms. TimeTaking 31.2