null Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ash-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ash-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ash-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-parrot-hancs ############### 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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-parrot-hancs/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 1373 and 0 Target number of residues in the AU: 1373 Target solvent content: 0.5773 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-2.1-parrot-hancs.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: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.75 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 1 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: 103.605 2.100 Wilson plot Bfac: 44.02 100147 reflections ( 99.19 % complete ) and 0 restraints for refining 13703 atoms. Observations/parameters ratio is 1.83 ------------------------------------------------------ Starting model: R = 0.3654 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3160 (Rfree = 0.000) for 13703 atoms. Found 277 (408 requested) and removed 225 (204 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.55 2.45 NCS extension: 0 residues added, 13755 seeds are put forward Round 1: 921 peptides, 143 chains. Longest chain 18 peptides. Score 0.498 Round 2: 1062 peptides, 110 chains. Longest chain 33 peptides. Score 0.692 Round 3: 1169 peptides, 95 chains. Longest chain 44 peptides. Score 0.777 Round 4: 1212 peptides, 78 chains. Longest chain 51 peptides. Score 0.824 Round 5: 1246 peptides, 75 chains. Longest chain 78 peptides. Score 0.840 Taking the results from Round 5 Chains 85, Residues 1171, Estimated correctness of the model 97.1 % 36 chains (860 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 41 A Built loop between residues 158 A and 163 A Built loop between residues 228 A and 232 A Built loop between residues 252 A and 260 A Built loop between residues 295 A and 299 A Built loop between residues 323 A and 327 A Built loop between residues 181 C and 185 C Built loop between residues 253 C and 259 C Built loop between residues 308 C and 311 C Built loop between residues 228 B and 234 B Built loop between residues 252 B and 256 B Built loop between residues 248 D and 257 D 69 chains (1209 residues) following loop building 24 chains (908 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 15834 restraints for refining 12117 atoms. 7359 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3333 (Rfree = 0.000) for 12117 atoms. Found 344 (361 requested) and removed 208 (180 requested) atoms. Cycle 2: After refmac, R = 0.3025 (Rfree = 0.000) for 12108 atoms. Found 276 (358 requested) and removed 187 (182 requested) atoms. Cycle 3: After refmac, R = 0.2858 (Rfree = 0.000) for 12126 atoms. Found 245 (348 requested) and removed 181 (181 requested) atoms. Cycle 4: After refmac, R = 0.2760 (Rfree = 0.000) for 12121 atoms. Found 201 (341 requested) and removed 116 (181 requested) atoms. Cycle 5: After refmac, R = 0.2684 (Rfree = 0.000) for 12154 atoms. Found 196 (334 requested) and removed 94 (181 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.45 2.35 NCS extension: 40 residues added (67 deleted due to clashes), 12323 seeds are put forward Round 1: 1240 peptides, 80 chains. Longest chain 101 peptides. Score 0.830 Round 2: 1274 peptides, 60 chains. Longest chain 96 peptides. Score 0.870 Round 3: 1292 peptides, 68 chains. Longest chain 106 peptides. Score 0.863 Round 4: 1274 peptides, 72 chains. Longest chain 66 peptides. Score 0.853 Round 5: 1284 peptides, 68 chains. Longest chain 103 peptides. Score 0.861 Taking the results from Round 2 Chains 67, Residues 1214, Estimated correctness of the model 98.0 % 29 chains (954 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 157 A and 164 A Built loop between residues 184 A and 187 A Built loop between residues 195 A and 198 A Built loop between residues 227 A and 232 A Built loop between residues 253 A and 257 A Built loop between residues 341 A and 351 A Built loop between residues 56 C and 59 C Built loop between residues 157 C and 164 C Built loop between residues 51 B and 59 B Built loop between residues 74 B and 78 B Built loop between residues 158 B and 161 B Built loop between residues 221 B and 232 B 51 chains (1260 residues) following loop building 16 chains (1012 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 14949 restraints for refining 12121 atoms. 5836 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2903 (Rfree = 0.000) for 12121 atoms. Found 289 (332 requested) and removed 211 (180 requested) atoms. Cycle 7: After refmac, R = 0.2680 (Rfree = 0.000) for 12136 atoms. Found 227 (327 requested) and removed 184 (181 requested) atoms. Cycle 8: After refmac, R = 0.2569 (Rfree = 0.000) for 12137 atoms. Found 182 (319 requested) and removed 181 (181 requested) atoms. Cycle 9: After refmac, R = 0.2506 (Rfree = 0.000) for 12109 atoms. Found 183 (310 requested) and removed 171 (180 requested) atoms. Cycle 10: After refmac, R = 0.2465 (Rfree = 0.000) for 12098 atoms. Found 184 (303 requested) and removed 125 (180 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.45 2.35 NCS extension: 141 residues added (166 deleted due to clashes), 12322 seeds are put forward Round 1: 1266 peptides, 62 chains. Longest chain 120 peptides. Score 0.865 Round 2: 1324 peptides, 48 chains. Longest chain 181 peptides. Score 0.897 Round 3: 1305 peptides, 58 chains. Longest chain 94 peptides. Score 0.880 Round 4: 1283 peptides, 66 chains. Longest chain 107 peptides. Score 0.864 Round 5: 1314 peptides, 56 chains. Longest chain 132 peptides. Score 0.885 Taking the results from Round 2 Chains 54, Residues 1276, Estimated correctness of the model 98.7 % 27 chains (1051 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 74 A and 78 A Built loop between residues 197 A and 200 A Built loop between residues 76 C and 82 C Built loop between residues 240 C and 244 C Built loop between residues 261 C and 266 C Built loop between residues 37 B and 40 B Built loop between residues 74 B and 79 B Built loop between residues 59 D and 68 D Built loop between residues 253 D and 257 D Built loop between residues 319 D and 327 D 39 chains (1311 residues) following loop building 16 chains (1094 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13755 restraints for refining 11970 atoms. 4170 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2844 (Rfree = 0.000) for 11970 atoms. Found 292 (292 requested) and removed 201 (178 requested) atoms. Cycle 12: After refmac, R = 0.2574 (Rfree = 0.000) for 12011 atoms. Found 287 (287 requested) and removed 180 (179 requested) atoms. Cycle 13: After refmac, R = 0.2450 (Rfree = 0.000) for 12102 atoms. Found 216 (282 requested) and removed 157 (180 requested) atoms. Cycle 14: After refmac, R = 0.2378 (Rfree = 0.000) for 12145 atoms. Found 212 (275 requested) and removed 122 (181 requested) atoms. Cycle 15: After refmac, R = 0.2328 (Rfree = 0.000) for 12223 atoms. Found 180 (269 requested) and removed 105 (182 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.44 2.34 NCS extension: 73 residues added (98 deleted due to clashes), 12393 seeds are put forward Round 1: 1293 peptides, 56 chains. Longest chain 108 peptides. Score 0.880 Round 2: 1318 peptides, 50 chains. Longest chain 113 peptides. Score 0.893 Round 3: 1316 peptides, 56 chains. Longest chain 111 peptides. Score 0.885 Round 4: 1321 peptides, 55 chains. Longest chain 174 peptides. Score 0.888 Round 5: 1325 peptides, 59 chains. Longest chain 100 peptides. Score 0.884 Taking the results from Round 2 Chains 56, Residues 1268, Estimated correctness of the model 98.6 % 27 chains (1075 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 204 A and 210 A Built loop between residues 238 A and 244 A Built loop between residues 266 A and 269 A Built loop between residues 74 C and 78 C Built loop between residues 75 B and 79 B Built loop between residues 221 B and 228 B 47 chains (1292 residues) following loop building 20 chains (1101 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 14176 restraints for refining 12105 atoms. 4569 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2678 (Rfree = 0.000) for 12105 atoms. Found 259 (259 requested) and removed 202 (180 requested) atoms. Cycle 17: After refmac, R = 0.2444 (Rfree = 0.000) for 12130 atoms. Found 253 (253 requested) and removed 179 (181 requested) atoms. Cycle 18: After refmac, R = 0.2345 (Rfree = 0.000) for 12191 atoms. Found 193 (247 requested) and removed 146 (181 requested) atoms. Cycle 19: After refmac, R = 0.2281 (Rfree = 0.000) for 12227 atoms. Found 188 (240 requested) and removed 109 (182 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 12293 atoms. Found 180 (234 requested) and removed 141 (183 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.45 2.35 NCS extension: 50 residues added (56 deleted due to clashes), 12393 seeds are put forward Round 1: 1301 peptides, 55 chains. Longest chain 106 peptides. Score 0.883 Round 2: 1341 peptides, 40 chains. Longest chain 289 peptides. Score 0.910 Round 3: 1327 peptides, 43 chains. Longest chain 174 peptides. Score 0.904 Round 4: 1318 peptides, 53 chains. Longest chain 156 peptides. Score 0.890 Round 5: 1304 peptides, 50 chains. Longest chain 119 peptides. Score 0.891 Taking the results from Round 2 Chains 46, Residues 1301, Estimated correctness of the model 99.0 % 23 chains (1137 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 37 A Built loop between residues 76 A and 87 A Built loop between residues 37 C and 40 C Built loop between residues 53 C and 56 C Built loop between residues 72 B and 82 B Built loop between residues 157 B and 162 B Built loop between residues 308 B and 311 B Built loop between residues 158 D and 162 D 35 chains (1325 residues) following loop building 15 chains (1171 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13597 restraints for refining 12169 atoms. 3490 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2615 (Rfree = 0.000) for 12169 atoms. Found 224 (224 requested) and removed 198 (181 requested) atoms. Cycle 22: After refmac, R = 0.2377 (Rfree = 0.000) for 12161 atoms. Found 218 (218 requested) and removed 181 (181 requested) atoms. Cycle 23: After refmac, R = 0.2273 (Rfree = 0.000) for 12184 atoms. Found 211 (211 requested) and removed 118 (181 requested) atoms. Cycle 24: After refmac, R = 0.2210 (Rfree = 0.000) for 12264 atoms. Found 204 (204 requested) and removed 104 (182 requested) atoms. Cycle 25: After refmac, R = 0.2163 (Rfree = 0.000) for 12352 atoms. Found 189 (199 requested) and removed 128 (184 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.44 2.34 NCS extension: 149 residues added (290 deleted due to clashes), 12571 seeds are put forward Round 1: 1317 peptides, 46 chains. Longest chain 175 peptides. Score 0.898 Round 2: 1345 peptides, 37 chains. Longest chain 273 peptides. Score 0.914 Round 3: 1319 peptides, 51 chains. Longest chain 123 peptides. Score 0.892 Round 4: 1327 peptides, 41 chains. Longest chain 176 peptides. Score 0.906 Round 5: 1324 peptides, 52 chains. Longest chain 100 peptides. Score 0.892 Taking the results from Round 2 Chains 43, Residues 1308, Estimated correctness of the model 99.1 % 23 chains (1214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 75 A and 78 A Built loop between residues 349 A and 352 A Built loop between residues 75 C and 82 C Built loop between residues 332 C and 335 C Built loop between residues 37 B and 40 B Built loop between residues 76 B and 87 B Built loop between residues 158 B and 161 B Built loop between residues 231 B and 234 B Built loop between residues 349 B and 352 B Built loop between residues 139 D and 150 D Built loop between residues 241 D and 249 D 29 chains (1347 residues) following loop building 11 chains (1263 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 12995 restraints for refining 12277 atoms. 2455 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2592 (Rfree = 0.000) for 12277 atoms. Found 190 (190 requested) and removed 200 (182 requested) atoms. Cycle 27: After refmac, R = 0.2349 (Rfree = 0.000) for 12241 atoms. Found 182 (182 requested) and removed 176 (182 requested) atoms. Cycle 28: After refmac, R = 0.2248 (Rfree = 0.000) for 12235 atoms. Found 182 (182 requested) and removed 114 (182 requested) atoms. Cycle 29: After refmac, R = 0.2209 (Rfree = 0.000) for 12296 atoms. Found 183 (183 requested) and removed 129 (183 requested) atoms. Cycle 30: After refmac, R = 0.2184 (Rfree = 0.000) for 12333 atoms. Found 184 (184 requested) and removed 153 (184 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.44 2.34 NCS extension: 70 residues added (257 deleted due to clashes), 12452 seeds are put forward Round 1: 1323 peptides, 38 chains. Longest chain 211 peptides. Score 0.909 Round 2: 1339 peptides, 30 chains. Longest chain 195 peptides. Score 0.921 Round 3: 1316 peptides, 37 chains. Longest chain 205 peptides. Score 0.909 Round 4: 1323 peptides, 40 chains. Longest chain 148 peptides. Score 0.907 Round 5: 1316 peptides, 47 chains. Longest chain 111 peptides. Score 0.897 Taking the results from Round 2 Chains 31, Residues 1309, Estimated correctness of the model 99.2 % 22 chains (1229 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 41 A Built loop between residues 53 A and 56 A Built loop between residues 75 A and 81 A Built loop between residues 75 C and 79 C Built loop between residues 178 C and 181 C Built loop between residues 54 B and 57 B Built loop between residues 75 B and 78 B Built loop between residues 141 B and 145 B Built loop between residues 159 B and 162 B Built loop between residues 179 B and 188 B Built loop between residues 241 B and 249 B Built loop between residues 341 D and 350 D 18 chains (1351 residues) following loop building 10 chains (1275 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 12959 restraints for refining 12321 atoms. 2342 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2599 (Rfree = 0.000) for 12321 atoms. Found 183 (183 requested) and removed 208 (183 requested) atoms. Cycle 32: After refmac, R = 0.2355 (Rfree = 0.000) for 12268 atoms. Found 183 (183 requested) and removed 183 (183 requested) atoms. Cycle 33: After refmac, R = 0.2251 (Rfree = 0.000) for 12252 atoms. Found 182 (182 requested) and removed 136 (182 requested) atoms. Cycle 34: After refmac, R = 0.2201 (Rfree = 0.000) for 12286 atoms. Found 183 (183 requested) and removed 131 (183 requested) atoms. Cycle 35: After refmac, R = 0.2169 (Rfree = 0.000) for 12326 atoms. Found 183 (183 requested) and removed 138 (183 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.44 2.34 NCS extension: 11 residues added (57 deleted due to clashes), 12394 seeds are put forward Round 1: 1315 peptides, 37 chains. Longest chain 211 peptides. Score 0.909 Round 2: 1332 peptides, 32 chains. Longest chain 158 peptides. Score 0.917 Round 3: 1330 peptides, 41 chains. Longest chain 121 peptides. Score 0.907 Round 4: 1329 peptides, 44 chains. Longest chain 119 peptides. Score 0.903 Round 5: 1323 peptides, 39 chains. Longest chain 204 peptides. Score 0.908 Taking the results from Round 2 Chains 36, Residues 1300, Estimated correctness of the model 99.1 % 24 chains (1225 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 41 A Built loop between residues 53 A and 56 A Built loop between residues 75 A and 78 A Built loop between residues 107 A and 116 A Built loop between residues 158 A and 163 A Built loop between residues 213 A and 216 A Built loop between residues 75 C and 78 C Built loop between residues 341 C and 345 C Built loop between residues 50 B and 56 B Built loop between residues 74 B and 78 B Built loop between residues 109 B and 114 B Built loop between residues 158 D and 161 D Built loop between residues 179 D and 190 D Built loop between residues 210 D and 213 D 21 chains (1349 residues) following loop building 10 chains (1276 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13266 restraints for refining 12286 atoms. 2672 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2556 (Rfree = 0.000) for 12286 atoms. Found 183 (183 requested) and removed 196 (183 requested) atoms. Cycle 37: After refmac, R = 0.2342 (Rfree = 0.000) for 12244 atoms. Found 182 (182 requested) and removed 182 (182 requested) atoms. Cycle 38: After refmac, R = 0.2247 (Rfree = 0.000) for 12236 atoms. Found 182 (182 requested) and removed 121 (182 requested) atoms. Cycle 39: After refmac, R = 0.2192 (Rfree = 0.000) for 12293 atoms. Found 183 (183 requested) and removed 103 (183 requested) atoms. Cycle 40: After refmac, R = 0.2158 (Rfree = 0.000) for 12367 atoms. Found 184 (184 requested) and removed 139 (184 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.44 2.34 NCS extension: 72 residues added (195 deleted due to clashes), 12492 seeds are put forward Round 1: 1335 peptides, 39 chains. Longest chain 161 peptides. Score 0.910 Round 2: 1352 peptides, 28 chains. Longest chain 230 peptides. Score 0.925 Round 3: 1338 peptides, 44 chains. Longest chain 148 peptides. Score 0.905 Round 4: 1340 peptides, 41 chains. Longest chain 215 peptides. Score 0.909 Round 5: 1305 peptides, 53 chains. Longest chain 102 peptides. Score 0.887 Taking the results from Round 2 Chains 31, Residues 1324, Estimated correctness of the model 99.3 % 21 chains (1236 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 75 A and 78 A Built loop between residues 108 A and 114 A Built loop between residues 342 A and 345 A Built loop between residues 170 C and 173 C Built loop between residues 37 B and 40 B Built loop between residues 72 B and 78 B Built loop between residues 301 B and 304 B Built loop between residues 157 D and 161 D Built loop between residues 243 D and 246 D Built loop between residues 272 D and 275 D 20 chains (1353 residues) following loop building 10 chains (1265 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13219 restraints for refining 12302 atoms. 2666 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2519 (Rfree = 0.000) for 12302 atoms. Found 183 (183 requested) and removed 191 (183 requested) atoms. Cycle 42: After refmac, R = 0.2298 (Rfree = 0.000) for 12275 atoms. Found 183 (183 requested) and removed 159 (183 requested) atoms. Cycle 43: After refmac, R = 0.2214 (Rfree = 0.000) for 12283 atoms. Found 183 (183 requested) and removed 113 (183 requested) atoms. Cycle 44: After refmac, R = 0.2161 (Rfree = 0.000) for 12347 atoms. Found 184 (184 requested) and removed 116 (184 requested) atoms. Cycle 45: After refmac, R = 0.2118 (Rfree = 0.000) for 12408 atoms. Found 185 (185 requested) and removed 132 (185 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.43 2.33 NCS extension: 31 residues added (209 deleted due to clashes), 12497 seeds are put forward Round 1: 1336 peptides, 33 chains. Longest chain 161 peptides. Score 0.917 Round 2: 1347 peptides, 30 chains. Longest chain 231 peptides. Score 0.922 Round 3: 1343 peptides, 36 chains. Longest chain 177 peptides. Score 0.915 Round 4: 1345 peptides, 42 chains. Longest chain 175 peptides. Score 0.908 Round 5: 1350 peptides, 42 chains. Longest chain 177 peptides. Score 0.909 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 1317, Estimated correctness of the model 99.2 % 23 chains (1255 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 33 A and 40 A Built loop between residues 75 A and 82 A Built loop between residues 161 A and 165 A Built loop between residues 211 A and 214 A Built loop between residues 37 C and 40 C Built loop between residues 76 C and 79 C Built loop between residues 109 C and 114 C Built loop between residues 288 C and 302 C Built loop between residues 37 B and 41 B Built loop between residues 52 B and 55 B Built loop between residues 76 B and 87 B Built loop between residues 109 B and 113 B Built loop between residues 342 B and 345 B Built loop between residues 106 D and 116 D Built loop between residues 158 D and 162 D Built loop between residues 178 D and 191 D Built loop between residues 211 D and 215 D Built loop between residues 226 D and 232 D 10 chains (1382 residues) following loop building 5 chains (1345 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 100147 reflections ( 99.19 % complete ) and 11029 restraints for refining 10802 atoms. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3096 (Rfree = 0.000) for 10802 atoms. Found 100 (161 requested) and removed 0 (161 requested) atoms. Cycle 47: After refmac, R = 0.2848 (Rfree = 0.000) for 10802 atoms. Found 66 (162 requested) and removed 1 (162 requested) atoms. Cycle 48: After refmac, R = 0.2702 (Rfree = 0.000) for 10802 atoms. Found 47 (163 requested) and removed 11 (163 requested) atoms. Cycle 49: After refmac, R = 0.2623 (Rfree = 0.000) for 10802 atoms. Found 31 (164 requested) and removed 10 (164 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:27:44 GMT 2018 Job finished. TimeTaking 184.97 Used memory is bytes: 28704016