Sun 23 Dec 23:49:29 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.6-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 ============================================================ Sun 23 Dec 23:49:33 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 82.21 4336 reflections ( 98.17 % complete ) and 0 restraints for refining 2729 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3373 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3272 (Rfree = 0.000) for 2729 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 0 residues added, 2786 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 11 peptides. Score 0.400 Round 2: 157 peptides, 21 chains. Longest chain 14 peptides. Score 0.507 Round 3: 175 peptides, 22 chains. Longest chain 17 peptides. Score 0.556 Round 4: 175 peptides, 22 chains. Longest chain 18 peptides. Score 0.556 Round 5: 177 peptides, 22 chains. Longest chain 22 peptides. Score 0.563 Taking the results from Round 5 Chains 22, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 4888 restraints for refining 2161 atoms. 4290 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2828 (Rfree = 0.000) for 2161 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 2: After refmac, R = 0.2659 (Rfree = 0.000) for 2127 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 3: After refmac, R = 0.2554 (Rfree = 0.000) for 2122 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2507 (Rfree = 0.000) for 2111 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2486 (Rfree = 0.000) for 2102 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2174 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 2204 seeds are put forward Round 1: 156 peptides, 22 chains. Longest chain 13 peptides. Score 0.486 Round 2: 164 peptides, 20 chains. Longest chain 16 peptides. Score 0.549 Round 3: 163 peptides, 20 chains. Longest chain 16 peptides. Score 0.546 Round 4: 164 peptides, 18 chains. Longest chain 25 peptides. Score 0.582 Round 5: 162 peptides, 18 chains. Longest chain 25 peptides. Score 0.575 Taking the results from Round 4 Chains 18, Residues 146, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 4802 restraints for refining 2111 atoms. 4236 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2645 (Rfree = 0.000) for 2111 atoms. Found 9 (13 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.2514 (Rfree = 0.000) for 2087 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2410 (Rfree = 0.000) for 2085 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2403 (Rfree = 0.000) for 2073 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2333 (Rfree = 0.000) for 2070 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2174 seeds are put forward Round 1: 144 peptides, 19 chains. Longest chain 16 peptides. Score 0.492 Round 2: 160 peptides, 19 chains. Longest chain 19 peptides. Score 0.552 Round 3: 171 peptides, 20 chains. Longest chain 25 peptides. Score 0.574 Round 4: 161 peptides, 16 chains. Longest chain 18 peptides. Score 0.603 Round 5: 176 peptides, 22 chains. Longest chain 26 peptides. Score 0.560 Taking the results from Round 4 Chains 16, Residues 145, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 4755 restraints for refining 2119 atoms. 4191 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2476 (Rfree = 0.000) for 2119 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.2317 (Rfree = 0.000) for 2119 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2234 (Rfree = 0.000) for 2116 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2172 (Rfree = 0.000) for 2113 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2129 (Rfree = 0.000) for 2101 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2148 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2163 seeds are put forward Round 1: 152 peptides, 23 chains. Longest chain 14 peptides. Score 0.452 Round 2: 165 peptides, 22 chains. Longest chain 15 peptides. Score 0.520 Round 3: 172 peptides, 22 chains. Longest chain 18 peptides. Score 0.546 Round 4: 163 peptides, 23 chains. Longest chain 17 peptides. Score 0.496 Round 5: 160 peptides, 22 chains. Longest chain 15 peptides. Score 0.501 Taking the results from Round 3 Chains 22, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 4721 restraints for refining 2138 atoms. 4143 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2336 (Rfree = 0.000) for 2138 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.2188 (Rfree = 0.000) for 2126 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2135 (Rfree = 0.000) for 2122 atoms. Found 2 (13 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.2105 (Rfree = 0.000) for 2112 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2100 (Rfree = 0.000) for 2106 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2195 seeds are put forward Round 1: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.371 Round 2: 159 peptides, 24 chains. Longest chain 12 peptides. Score 0.463 Round 3: 156 peptides, 21 chains. Longest chain 19 peptides. Score 0.503 Round 4: 148 peptides, 22 chains. Longest chain 14 peptides. Score 0.454 Round 5: 153 peptides, 17 chains. Longest chain 20 peptides. Score 0.560 Taking the results from Round 5 Chains 17, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 4961 restraints for refining 2188 atoms. 4434 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2352 (Rfree = 0.000) for 2188 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.2161 (Rfree = 0.000) for 2182 atoms. Found 9 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2192 (Rfree = 0.000) for 2172 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2262 (Rfree = 0.000) for 2171 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2135 (Rfree = 0.000) for 2173 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 2253 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2281 seeds are put forward Round 1: 136 peptides, 22 chains. Longest chain 14 peptides. Score 0.404 Round 2: 149 peptides, 22 chains. Longest chain 13 peptides. Score 0.458 Round 3: 155 peptides, 21 chains. Longest chain 18 peptides. Score 0.500 Round 4: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.472 Round 5: 155 peptides, 22 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 3 Chains 21, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5117 restraints for refining 2233 atoms. 4602 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2200 (Rfree = 0.000) for 2233 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 27: After refmac, R = 0.2016 (Rfree = 0.000) for 2219 atoms. Found 4 (14 requested) and removed 14 (7 requested) atoms. Cycle 28: After refmac, R = 0.2641 (Rfree = 0.000) for 2205 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 29: After refmac, R = 0.2448 (Rfree = 0.000) for 2189 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 30: After refmac, R = 0.2022 (Rfree = 0.000) for 2181 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 0 residues added, 2259 seeds are put forward Round 1: 124 peptides, 22 chains. Longest chain 15 peptides. Score 0.350 Round 2: 138 peptides, 19 chains. Longest chain 16 peptides. Score 0.468 Round 3: 127 peptides, 20 chains. Longest chain 17 peptides. Score 0.403 Round 4: 138 peptides, 19 chains. Longest chain 17 peptides. Score 0.468 Round 5: 128 peptides, 19 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 4 Chains 19, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5321 restraints for refining 2222 atoms. 4864 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2077 (Rfree = 0.000) for 2222 atoms. Found 6 (14 requested) and removed 17 (7 requested) atoms. Cycle 32: After refmac, R = 0.2152 (Rfree = 0.000) for 2199 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.2129 (Rfree = 0.000) for 2191 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2110 (Rfree = 0.000) for 2188 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1786 (Rfree = 0.000) for 2174 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 2249 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2282 seeds are put forward Round 1: 126 peptides, 23 chains. Longest chain 15 peptides. Score 0.340 Round 2: 142 peptides, 21 chains. Longest chain 14 peptides. Score 0.448 Round 3: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.456 Round 4: 141 peptides, 21 chains. Longest chain 21 peptides. Score 0.444 Round 5: 149 peptides, 21 chains. Longest chain 21 peptides. Score 0.476 Taking the results from Round 5 Chains 21, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5174 restraints for refining 2233 atoms. 4683 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 2233 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.1983 (Rfree = 0.000) for 2221 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.2012 (Rfree = 0.000) for 2213 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1952 (Rfree = 0.000) for 2207 atoms. Found 3 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.1808 (Rfree = 0.000) for 2195 atoms. Found 0 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2297 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 2334 seeds are put forward Round 1: 118 peptides, 22 chains. Longest chain 11 peptides. Score 0.322 Round 2: 128 peptides, 23 chains. Longest chain 11 peptides. Score 0.349 Round 3: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.389 Round 4: 134 peptides, 20 chains. Longest chain 12 peptides. Score 0.433 Round 5: 136 peptides, 22 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 20, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5176 restraints for refining 2233 atoms. 4740 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2003 (Rfree = 0.000) for 2233 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 42: After refmac, R = 0.1939 (Rfree = 0.000) for 2228 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 2224 atoms. Found 8 (14 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.1687 (Rfree = 0.000) for 2211 atoms. Found 4 (14 requested) and removed 15 (7 requested) atoms. Cycle 45: After refmac, R = 0.1735 (Rfree = 0.000) for 2195 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.40 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 0 residues added, 2248 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 12 peptides. Score 0.309 Round 2: 120 peptides, 20 chains. Longest chain 15 peptides. Score 0.372 Round 3: 123 peptides, 19 chains. Longest chain 17 peptides. Score 0.405 Round 4: 117 peptides, 17 chains. Longest chain 18 peptides. Score 0.418 Round 5: 127 peptides, 21 chains. Longest chain 16 peptides. Score 0.384 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 100, 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 5360 restraints for refining 2233 atoms. 4977 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1916 (Rfree = 0.000) for 2233 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1787 (Rfree = 0.000) for 2223 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1926 (Rfree = 0.000) for 2215 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2076 (Rfree = 0.000) for 2206 atoms. TimeTaking 28.12