Sun 23 Dec 23:49:52 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 2ash-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-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/2ash-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-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 23:49:57 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/2ash-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-2.1-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 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-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: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-2.1-parrot-mrncs.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 13731 atoms. Observations/parameters ratio is 1.82 ------------------------------------------------------ Starting model: R = 0.3611 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3071 (Rfree = 0.000) for 13731 atoms. Found 280 (409 requested) and removed 217 (204 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.52 2.42 NCS extension: 0 residues added, 13794 seeds are put forward Round 1: 998 peptides, 136 chains. Longest chain 23 peptides. Score 0.579 Round 2: 1148 peptides, 108 chains. Longest chain 50 peptides. Score 0.740 Round 3: 1213 peptides, 81 chains. Longest chain 54 peptides. Score 0.819 Round 4: 1264 peptides, 64 chains. Longest chain 68 peptides. Score 0.862 Round 5: 1283 peptides, 72 chains. Longest chain 56 peptides. Score 0.855 Taking the results from Round 4 Chains 73, Residues 1200, Estimated correctness of the model 97.8 % 32 chains (928 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 42 A Built loop between residues 75 A and 79 A Built loop between residues 182 A and 185 A Built loop between residues 218 A and 225 A Built loop between residues 249 A and 256 A Built loop between residues 296 A and 305 A Built loop between residues 156 C and 166 C Built loop between residues 302 C and 308 C Built loop between residues 50 B and 56 B Built loop between residues 74 B and 80 B Built loop between residues 222 B and 226 B Built loop between residues 253 B and 263 B Built loop between residues 296 B and 299 B Built loop between residues 337 B and 347 B Built loop between residues 253 D and 257 D Built loop between residues 273 D and 278 D 49 chains (1260 residues) following loop building 16 chains (1015 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 15494 restraints for refining 12430 atoms. 6358 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3300 (Rfree = 0.000) for 12430 atoms. Found 369 (370 requested) and removed 224 (185 requested) atoms. Cycle 2: After refmac, R = 0.3014 (Rfree = 0.000) for 12438 atoms. Found 248 (367 requested) and removed 192 (187 requested) atoms. Cycle 3: After refmac, R = 0.2861 (Rfree = 0.000) for 12404 atoms. Found 215 (357 requested) and removed 187 (186 requested) atoms. Cycle 4: After refmac, R = 0.2748 (Rfree = 0.000) for 12375 atoms. Found 193 (348 requested) and removed 169 (185 requested) atoms. Cycle 5: After refmac, R = 0.2682 (Rfree = 0.000) for 12359 atoms. Found 174 (339 requested) and removed 118 (184 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.45 2.35 NCS extension: 6 residues added (33 deleted due to clashes), 12447 seeds are put forward Round 1: 1255 peptides, 78 chains. Longest chain 59 peptides. Score 0.838 Round 2: 1311 peptides, 53 chains. Longest chain 98 peptides. Score 0.888 Round 3: 1323 peptides, 53 chains. Longest chain 146 peptides. Score 0.891 Round 4: 1338 peptides, 57 chains. Longest chain 124 peptides. Score 0.889 Round 5: 1332 peptides, 52 chains. Longest chain 129 peptides. Score 0.894 Taking the results from Round 5 Chains 61, Residues 1280, Estimated correctness of the model 98.6 % 31 chains (1130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 72 A and 80 A Built loop between residues 199 A and 202 A Built loop between residues 328 A and 331 A Built loop between residues 59 C and 62 C Built loop between residues 74 C and 79 C Built loop between residues 240 C and 244 C Built loop between residues 253 C and 257 C Built loop between residues 298 C and 305 C Built loop between residues 333 C and 336 C Built loop between residues 349 C and 353 C Built loop between residues 76 B and 84 B Built loop between residues 183 B and 186 B Built loop between residues 202 B and 213 B Built loop between residues 251 B and 255 B Built loop between residues 275 B and 280 B Built loop between residues 114 D and 119 D Built loop between residues 333 D and 336 D 37 chains (1333 residues) following loop building 13 chains (1198 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13656 restraints for refining 12364 atoms. 3434 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2937 (Rfree = 0.000) for 12364 atoms. Found 322 (331 requested) and removed 207 (184 requested) atoms. Cycle 7: After refmac, R = 0.2674 (Rfree = 0.000) for 12428 atoms. Found 232 (326 requested) and removed 186 (185 requested) atoms. Cycle 8: After refmac, R = 0.2563 (Rfree = 0.000) for 12424 atoms. Found 221 (319 requested) and removed 186 (185 requested) atoms. Cycle 9: After refmac, R = 0.2493 (Rfree = 0.000) for 12430 atoms. Found 207 (312 requested) and removed 155 (185 requested) atoms. Cycle 10: After refmac, R = 0.2451 (Rfree = 0.000) for 12462 atoms. Found 195 (305 requested) and removed 140 (186 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.44 2.34 NCS extension: 167 residues added (238 deleted due to clashes), 12708 seeds are put forward Round 1: 1331 peptides, 49 chains. Longest chain 178 peptides. Score 0.897 Round 2: 1344 peptides, 42 chains. Longest chain 175 peptides. Score 0.908 Round 3: 1334 peptides, 49 chains. Longest chain 105 peptides. Score 0.898 Round 4: 1332 peptides, 53 chains. Longest chain 135 peptides. Score 0.893 Round 5: 1317 peptides, 60 chains. Longest chain 86 peptides. Score 0.880 Taking the results from Round 2 Chains 50, Residues 1302, Estimated correctness of the model 98.9 % 24 chains (1167 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 254 A and 257 A Built loop between residues 71 C and 78 C Built loop between residues 109 C and 114 C Built loop between residues 228 B and 238 B Built loop between residues 342 B and 345 B Built loop between residues 103 D and 114 D Built loop between residues 158 D and 161 D Built loop between residues 182 D and 185 D Built loop between residues 230 D and 238 D Built loop between residues 296 D and 301 D 34 chains (1347 residues) following loop building 12 chains (1219 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13624 restraints for refining 12413 atoms. 3234 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2750 (Rfree = 0.000) for 12413 atoms. Found 274 (296 requested) and removed 208 (185 requested) atoms. Cycle 12: After refmac, R = 0.2504 (Rfree = 0.000) for 12435 atoms. Found 257 (290 requested) and removed 186 (186 requested) atoms. Cycle 13: After refmac, R = 0.2384 (Rfree = 0.000) for 12484 atoms. Found 182 (283 requested) and removed 169 (186 requested) atoms. Cycle 14: After refmac, R = 0.2322 (Rfree = 0.000) for 12479 atoms. Found 185 (275 requested) and removed 132 (186 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 12509 atoms. Found 186 (269 requested) and removed 124 (186 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.45 2.35 NCS extension: 131 residues added (218 deleted due to clashes), 12714 seeds are put forward Round 1: 1342 peptides, 42 chains. Longest chain 150 peptides. Score 0.908 Round 2: 1374 peptides, 33 chains. Longest chain 163 peptides. Score 0.923 Round 3: 1367 peptides, 44 chains. Longest chain 178 peptides. Score 0.910 Round 4: 1338 peptides, 48 chains. Longest chain 132 peptides. Score 0.900 Round 5: 1341 peptides, 44 chains. Longest chain 140 peptides. Score 0.905 Taking the results from Round 2 Chains 33, Residues 1341, Estimated correctness of the model 99.2 % 23 chains (1254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 107 A and 114 A Built loop between residues 229 A and 232 A Built loop between residues 342 A and 345 A Built loop between residues 252 C and 259 C Built loop between residues 324 C and 327 C Built loop between residues 209 B and 213 B Built loop between residues 45 D and 49 D Built loop between residues 115 D and 118 D Built loop between residues 157 D and 165 D Built loop between residues 184 D and 190 D Built loop between residues 212 D and 215 D Built loop between residues 255 D and 258 D 20 chains (1384 residues) following loop building 10 chains (1298 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13189 restraints for refining 12617 atoms. 2377 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2751 (Rfree = 0.000) for 12617 atoms. Found 263 (263 requested) and removed 243 (188 requested) atoms. Cycle 17: After refmac, R = 0.2474 (Rfree = 0.000) for 12605 atoms. Found 243 (256 requested) and removed 188 (188 requested) atoms. Cycle 18: After refmac, R = 0.2364 (Rfree = 0.000) for 12631 atoms. Found 211 (249 requested) and removed 191 (188 requested) atoms. Cycle 19: After refmac, R = 0.2304 (Rfree = 0.000) for 12632 atoms. Found 223 (241 requested) and removed 189 (188 requested) atoms. Cycle 20: After refmac, R = 0.2273 (Rfree = 0.000) for 12649 atoms. Found 188 (234 requested) and removed 190 (188 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.45 2.35 NCS extension: 107 residues added (95 deleted due to clashes), 12770 seeds are put forward Round 1: 1356 peptides, 40 chains. Longest chain 116 peptides. Score 0.912 Round 2: 1372 peptides, 32 chains. Longest chain 183 peptides. Score 0.924 Round 3: 1353 peptides, 48 chains. Longest chain 135 peptides. Score 0.903 Round 4: 1355 peptides, 50 chains. Longest chain 129 peptides. Score 0.901 Round 5: 1347 peptides, 47 chains. Longest chain 131 peptides. Score 0.903 Taking the results from Round 2 Chains 34, Residues 1340, Estimated correctness of the model 99.3 % 24 chains (1293 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 214 A and 217 A Built loop between residues 253 A and 256 A Built loop between residues 38 C and 41 C Built loop between residues 53 C and 56 C Built loop between residues 76 C and 78 C Built loop between residues 158 C and 161 C Built loop between residues 252 C and 256 C Built loop between residues 272 C and 275 C Built loop between residues 37 B and 40 B Built loop between residues 71 B and 78 B Built loop between residues 157 B and 161 B Built loop between residues 342 B and 345 B Built loop between residues 185 D and 189 D Built loop between residues 273 D and 276 D 17 chains (1375 residues) following loop building 8 chains (1331 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13041 restraints for refining 12483 atoms. 2112 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2759 (Rfree = 0.000) for 12483 atoms. Found 223 (223 requested) and removed 205 (186 requested) atoms. Cycle 22: After refmac, R = 0.2435 (Rfree = 0.000) for 12489 atoms. Found 216 (216 requested) and removed 186 (186 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2326 (Rfree = 0.000) for 12485 atoms. Found 209 (209 requested) and removed 142 (186 requested) atoms. Cycle 24: After refmac, R = 0.2258 (Rfree = 0.000) for 12532 atoms. Found 202 (202 requested) and removed 130 (187 requested) atoms. Cycle 25: After refmac, R = 0.2213 (Rfree = 0.000) for 12588 atoms. Found 195 (195 requested) and removed 133 (187 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.44 2.34 NCS extension: 41 residues added (116 deleted due to clashes), 12697 seeds are put forward Round 1: 1377 peptides, 35 chains. Longest chain 214 peptides. Score 0.921 Round 2: 1373 peptides, 37 chains. Longest chain 214 peptides. Score 0.919 Round 3: 1364 peptides, 48 chains. Longest chain 100 peptides. Score 0.905 Round 4: 1382 peptides, 39 chains. Longest chain 298 peptides. Score 0.918 Round 5: 1369 peptides, 46 chains. Longest chain 159 peptides. Score 0.908 Taking the results from Round 1 Chains 41, Residues 1342, Estimated correctness of the model 99.2 % 25 chains (1263 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 41 A Built loop between residues 53 A and 56 A Built loop between residues 76 A and 78 A Built loop between residues 110 A and 114 A Built loop between residues 157 A and 164 A Built loop between residues 37 C and 40 C Built loop between residues 72 C and 78 C Built loop between residues 109 C and 114 C Built loop between residues 230 C and 233 C Built loop between residues 252 C and 256 C Built loop between residues 36 B and 40 B Built loop between residues 75 B and 78 B Built loop between residues 183 B and 186 B Built loop between residues 213 B and 216 B Built loop between residues 254 B and 258 B Built loop between residues 272 B and 275 B Built loop between residues 108 D and 112 D 18 chains (1379 residues) following loop building 8 chains (1311 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13081 restraints for refining 12445 atoms. 2221 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2574 (Rfree = 0.000) for 12445 atoms. Found 185 (185 requested) and removed 202 (185 requested) atoms. Cycle 27: After refmac, R = 0.2346 (Rfree = 0.000) for 12385 atoms. Found 185 (185 requested) and removed 185 (185 requested) atoms. Cycle 28: After refmac, R = 0.2277 (Rfree = 0.000) for 12376 atoms. Found 184 (184 requested) and removed 134 (184 requested) atoms. Cycle 29: After refmac, R = 0.2223 (Rfree = 0.000) for 12409 atoms. Found 185 (185 requested) and removed 122 (185 requested) atoms. Cycle 30: After refmac, R = 0.2183 (Rfree = 0.000) for 12461 atoms. Found 185 (185 requested) and removed 149 (185 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.44 2.34 NCS extension: 76 residues added (192 deleted due to clashes), 12582 seeds are put forward Round 1: 1347 peptides, 38 chains. Longest chain 118 peptides. Score 0.913 Round 2: 1365 peptides, 33 chains. Longest chain 181 peptides. Score 0.922 Round 3: 1355 peptides, 43 chains. Longest chain 129 peptides. Score 0.909 Round 4: 1349 peptides, 48 chains. Longest chain 143 peptides. Score 0.902 Round 5: 1366 peptides, 43 chains. Longest chain 138 peptides. Score 0.911 Taking the results from Round 2 Chains 35, Residues 1332, Estimated correctness of the model 99.2 % 25 chains (1264 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 40 A Built loop between residues 75 A and 78 A Built loop between residues 157 A and 163 A Built loop between residues 342 A and 345 A Built loop between residues 74 C and 78 C Built loop between residues 214 C and 217 C Built loop between residues 253 C and 256 C Built loop between residues 37 B and 41 B Built loop between residues 53 B and 56 B Built loop between residues 71 B and 78 B Built loop between residues 158 B and 161 B Built loop between residues 230 B and 233 B Built loop between residues 251 B and 255 B Built loop between residues 296 B and 301 B Built loop between residues 108 D and 118 D Built loop between residues 184 D and 188 D Built loop between residues 196 D and 199 D Built loop between residues 236 D and 239 D Built loop between residues 272 D and 275 D 14 chains (1386 residues) following loop building 6 chains (1323 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 12810 restraints for refining 12378 atoms. 1871 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2585 (Rfree = 0.000) for 12378 atoms. Found 184 (184 requested) and removed 198 (184 requested) atoms. Cycle 32: After refmac, R = 0.2344 (Rfree = 0.000) for 12337 atoms. Found 184 (184 requested) and removed 185 (184 requested) atoms. Cycle 33: After refmac, R = 0.2265 (Rfree = 0.000) for 12324 atoms. Found 183 (183 requested) and removed 139 (183 requested) atoms. Cycle 34: After refmac, R = 0.2214 (Rfree = 0.000) for 12362 atoms. Found 184 (184 requested) and removed 146 (184 requested) atoms. Cycle 35: After refmac, R = 0.2186 (Rfree = 0.000) for 12389 atoms. Found 184 (184 requested) and removed 147 (184 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.44 2.34 NCS extension: 14 residues added (370 deleted due to clashes), 12453 seeds are put forward Round 1: 1351 peptides, 39 chains. Longest chain 112 peptides. Score 0.913 Round 2: 1367 peptides, 32 chains. Longest chain 154 peptides. Score 0.923 Round 3: 1361 peptides, 48 chains. Longest chain 120 peptides. Score 0.904 Round 4: 1356 peptides, 40 chains. Longest chain 156 peptides. Score 0.912 Round 5: 1331 peptides, 49 chains. Longest chain 137 peptides. Score 0.897 Taking the results from Round 2 Chains 35, Residues 1335, Estimated correctness of the model 99.2 % 23 chains (1227 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 157 A and 162 A Built loop between residues 205 A and 209 A Built loop between residues 342 A and 345 A Built loop between residues 216 C and 220 C Built loop between residues 252 C and 257 C Built loop between residues 37 B and 40 B Built loop between residues 75 B and 78 B Built loop between residues 230 B and 233 B Built loop between residues 252 B and 255 B Built loop between residues 286 B and 289 B Built loop between residues 341 B and 345 B Built loop between residues 229 D and 232 D 19 chains (1367 residues) following loop building 9 chains (1262 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 13449 restraints for refining 12322 atoms. 2788 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2560 (Rfree = 0.000) for 12322 atoms. Found 183 (183 requested) and removed 197 (183 requested) atoms. Cycle 37: After refmac, R = 0.2333 (Rfree = 0.000) for 12287 atoms. Found 183 (183 requested) and removed 183 (183 requested) atoms. Cycle 38: After refmac, R = 0.2255 (Rfree = 0.000) for 12272 atoms. Found 183 (183 requested) and removed 89 (183 requested) atoms. Cycle 39: After refmac, R = 0.2194 (Rfree = 0.000) for 12357 atoms. Found 184 (184 requested) and removed 100 (184 requested) atoms. Cycle 40: After refmac, R = 0.2157 (Rfree = 0.000) for 12435 atoms. Found 185 (185 requested) and removed 114 (185 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.44 2.34 NCS extension: 8 residues added (72 deleted due to clashes), 12517 seeds are put forward Round 1: 1355 peptides, 35 chains. Longest chain 260 peptides. Score 0.918 Round 2: 1374 peptides, 34 chains. Longest chain 180 peptides. Score 0.922 Round 3: 1362 peptides, 39 chains. Longest chain 159 peptides. Score 0.915 Round 4: 1357 peptides, 48 chains. Longest chain 121 peptides. Score 0.904 Round 5: 1340 peptides, 41 chains. Longest chain 127 peptides. Score 0.909 Taking the results from Round 2 Chains 36, Residues 1340, Estimated correctness of the model 99.2 % 24 chains (1270 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 178 A and 182 A Built loop between residues 37 C and 40 C Built loop between residues 75 C and 79 C Built loop between residues 104 C and 107 C Built loop between residues 230 C and 233 C Built loop between residues 253 C and 256 C Built loop between residues 299 C and 302 C Built loop between residues 37 B and 40 B Built loop between residues 75 B and 78 B Built loop between residues 109 B and 116 B Built loop between residues 195 B and 198 B Built loop between residues 295 B and 298 B Built loop between residues 342 B and 345 B Built loop between residues 48 D and 56 D Built loop between residues 157 D and 162 D Built loop between residues 178 D and 185 D 15 chains (1385 residues) following loop building 6 chains (1323 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 12828 restraints for refining 12385 atoms. 1883 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2531 (Rfree = 0.000) for 12385 atoms. Found 184 (184 requested) and removed 197 (184 requested) atoms. Cycle 42: After refmac, R = 0.2321 (Rfree = 0.000) for 12347 atoms. Found 184 (184 requested) and removed 167 (184 requested) atoms. Cycle 43: After refmac, R = 0.2243 (Rfree = 0.000) for 12353 atoms. Found 184 (184 requested) and removed 108 (184 requested) atoms. Cycle 44: After refmac, R = 0.2193 (Rfree = 0.000) for 12420 atoms. Found 185 (185 requested) and removed 113 (185 requested) atoms. Cycle 45: After refmac, R = 0.2165 (Rfree = 0.000) for 12482 atoms. Found 186 (186 requested) and removed 108 (186 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.34 NCS extension: 56 residues added (185 deleted due to clashes), 12623 seeds are put forward Round 1: 1364 peptides, 38 chains. Longest chain 214 peptides. Score 0.916 Round 2: 1373 peptides, 31 chains. Longest chain 292 peptides. Score 0.925 Round 3: 1361 peptides, 39 chains. Longest chain 156 peptides. Score 0.914 Round 4: 1360 peptides, 42 chains. Longest chain 113 peptides. Score 0.911 Round 5: 1356 peptides, 39 chains. Longest chain 124 peptides. Score 0.914 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 1342, Estimated correctness of the model 99.3 % 23 chains (1266 residues) have been docked in sequence Sequence coverage is 94 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 75 A and 78 A Built loop between residues 157 A and 161 A Built loop between residues 37 C and 41 C Built loop between residues 53 C and 56 C Built loop between residues 76 C and 78 C Built loop between residues 37 B and 40 B Built loop between residues 53 B and 56 B Built loop between residues 75 B and 78 B Built loop between residues 195 B and 198 B Built loop between residues 342 B and 345 B Built loop between residues 360 B and 363 B Built loop between residues 37 D and 50 D Built loop between residues 158 D and 162 D Built loop between residues 178 D and 186 D 19 chains (1383 residues) following loop building 9 chains (1311 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 100147 reflections ( 99.19 % complete ) and 10886 restraints for refining 10667 atoms. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3154 (Rfree = 0.000) for 10667 atoms. Found 120 (158 requested) and removed 0 (158 requested) atoms. Cycle 47: After refmac, R = 0.2915 (Rfree = 0.000) for 10667 atoms. Found 70 (160 requested) and removed 5 (160 requested) atoms. Cycle 48: After refmac, R = 0.2781 (Rfree = 0.000) for 10667 atoms. Found 42 (161 requested) and removed 9 (161 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2702 (Rfree = 0.000) for 10667 atoms. TimeTaking 177.92