Sun 23 Dec 22:23:13 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 1vkn-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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/1vkn-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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 22:23:22 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/1vkn-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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 1216 and 0 Target number of residues in the AU: 1216 Target solvent content: 0.5516 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-2.5-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.60 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: 93.562 2.450 Wilson plot Bfac: 35.96 52490 reflections ( 98.47 % complete ) and 0 restraints for refining 12385 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Starting model: R = 0.3047 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2143 (Rfree = 0.000) for 12385 atoms. Found 233 (237 requested) and removed 148 (118 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.46 2.53 NCS extension: 0 residues added, 12470 seeds are put forward Round 1: 861 peptides, 131 chains. Longest chain 17 peptides. Score 0.537 Round 2: 995 peptides, 96 chains. Longest chain 45 peptides. Score 0.745 Round 3: 1073 peptides, 71 chains. Longest chain 70 peptides. Score 0.836 Round 4: 1093 peptides, 68 chains. Longest chain 54 peptides. Score 0.848 Round 5: 1129 peptides, 50 chains. Longest chain 93 peptides. Score 0.888 Taking the results from Round 5 Chains 56, Residues 1079, Estimated correctness of the model 97.5 % 26 chains (857 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 93 A and 101 A Built loop between residues 228 A and 234 A Built loop between residues 274 A and 277 A Built loop between residues 292 A and 295 A Built loop between residues 307 A and 311 A Built loop between residues 135 C and 138 C Built loop between residues 189 C and 200 C Built loop between residues 256 C and 259 C Built loop between residues 161 B and 164 B Built loop between residues 321 B and 325 B 41 chains (1115 residues) following loop building 15 chains (897 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 13482 restraints for refining 10776 atoms. 5472 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2487 (Rfree = 0.000) for 10776 atoms. Found 195 (207 requested) and removed 137 (103 requested) atoms. Cycle 2: After refmac, R = 0.2198 (Rfree = 0.000) for 10717 atoms. Found 130 (204 requested) and removed 112 (104 requested) atoms. Cycle 3: After refmac, R = 0.2085 (Rfree = 0.000) for 10673 atoms. Found 106 (198 requested) and removed 110 (103 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2020 (Rfree = 0.000) for 10642 atoms. Found 95 (192 requested) and removed 108 (102 requested) atoms. Cycle 5: After refmac, R = 0.1968 (Rfree = 0.000) for 10613 atoms. Found 92 (188 requested) and removed 103 (102 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.50 2.57 NCS extension: 386 residues added (888 deleted due to clashes), 11017 seeds are put forward Round 1: 1145 peptides, 44 chains. Longest chain 150 peptides. Score 0.901 Round 2: 1179 peptides, 41 chains. Longest chain 112 peptides. Score 0.912 Round 3: 1179 peptides, 42 chains. Longest chain 123 peptides. Score 0.911 Round 4: 1177 peptides, 50 chains. Longest chain 65 peptides. Score 0.900 Round 5: 1177 peptides, 47 chains. Longest chain 81 peptides. Score 0.904 Taking the results from Round 2 Chains 47, Residues 1138, Estimated correctness of the model 98.4 % 25 chains (1009 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 320 A and 327 A Built loop between residues 85 C and 89 C Built loop between residues 191 C and 200 C Built loop between residues 308 C and 311 C Built loop between residues 327 C and 330 C Built loop between residues 73 B and 76 B Built loop between residues 97 B and 100 B Built loop between residues 159 B and 162 B Built loop between residues 188 B and 198 B Built loop between residues 308 B and 311 B Built loop between residues 331 B and 334 B Built loop between residues 220 D and 224 D Built loop between residues 292 D and 295 D Built loop between residues 324 D and 328 D 32 chains (1183 residues) following loop building 11 chains (1057 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11948 restraints for refining 10661 atoms. 2977 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2247 (Rfree = 0.000) for 10661 atoms. Found 184 (184 requested) and removed 125 (102 requested) atoms. Cycle 7: After refmac, R = 0.2024 (Rfree = 0.000) for 10690 atoms. Found 145 (180 requested) and removed 105 (102 requested) atoms. Cycle 8: After refmac, R = 0.1938 (Rfree = 0.000) for 10714 atoms. Found 102 (177 requested) and removed 105 (103 requested) atoms. Cycle 9: After refmac, R = 0.1887 (Rfree = 0.000) for 10702 atoms. Found 95 (172 requested) and removed 106 (102 requested) atoms. Cycle 10: After refmac, R = 0.1856 (Rfree = 0.000) for 10682 atoms. Found 100 (168 requested) and removed 106 (102 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.49 2.56 NCS extension: 1044 residues added (1297 deleted due to clashes), 11743 seeds are put forward Round 1: 1186 peptides, 39 chains. Longest chain 174 peptides. Score 0.916 Round 2: 1201 peptides, 41 chains. Longest chain 89 peptides. Score 0.916 Round 3: 1194 peptides, 44 chains. Longest chain 102 peptides. Score 0.911 Round 4: 1177 peptides, 51 chains. Longest chain 106 peptides. Score 0.898 Round 5: 1188 peptides, 46 chains. Longest chain 71 peptides. Score 0.907 Taking the results from Round 2 Chains 43, Residues 1160, Estimated correctness of the model 98.5 % 27 chains (1031 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 174 A and 177 A Built loop between residues 189 A and 200 A Built loop between residues 93 C and 96 C Built loop between residues 153 C and 156 C Built loop between residues 190 C and 199 C Built loop between residues 244 C and 247 C Built loop between residues 256 C and 259 C Built loop between residues 289 C and 292 C Built loop between residues 188 B and 196 B Built loop between residues 265 B and 269 B Built loop between residues 308 B and 311 B Built loop between residues 108 D and 111 D Built loop between residues 190 D and 197 D Built loop between residues 256 D and 259 D Built loop between residues 332 D and 335 D 28 chains (1214 residues) following loop building 12 chains (1085 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 12203 restraints for refining 10886 atoms. 2985 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 10886 atoms. Found 167 (167 requested) and removed 150 (104 requested) atoms. Cycle 12: After refmac, R = 0.1970 (Rfree = 0.000) for 10874 atoms. Found 163 (163 requested) and removed 109 (104 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1859 (Rfree = 0.000) for 10913 atoms. Found 110 (159 requested) and removed 111 (104 requested) atoms. Cycle 14: After refmac, R = 0.1812 (Rfree = 0.000) for 10905 atoms. Found 104 (155 requested) and removed 106 (104 requested) atoms. Cycle 15: After refmac, R = 0.1775 (Rfree = 0.000) for 10897 atoms. Found 112 (150 requested) and removed 109 (104 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.49 2.56 NCS extension: 107 residues added (264 deleted due to clashes), 11023 seeds are put forward Round 1: 1185 peptides, 42 chains. Longest chain 115 peptides. Score 0.912 Round 2: 1198 peptides, 36 chains. Longest chain 114 peptides. Score 0.922 Round 3: 1199 peptides, 39 chains. Longest chain 154 peptides. Score 0.918 Round 4: 1195 peptides, 44 chains. Longest chain 96 peptides. Score 0.911 Round 5: 1180 peptides, 47 chains. Longest chain 129 peptides. Score 0.904 Taking the results from Round 2 Chains 38, Residues 1162, Estimated correctness of the model 98.7 % 25 chains (1078 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 190 A and 199 A Built loop between residues 128 C and 131 C Built loop between residues 148 C and 151 C Built loop between residues 185 C and 196 C Built loop between residues 308 C and 311 C Built loop between residues 292 B and 295 B Built loop between residues 308 B and 311 B Built loop between residues 320 B and 323 B Built loop between residues 328 B and 334 B Built loop between residues 91 D and 95 D Built loop between residues 107 D and 110 D Built loop between residues 159 D and 162 D Built loop between residues 230 D and 233 D Built loop between residues 242 D and 245 D 24 chains (1208 residues) following loop building 11 chains (1124 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11787 restraints for refining 10759 atoms. 2430 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2121 (Rfree = 0.000) for 10759 atoms. Found 144 (144 requested) and removed 129 (103 requested) atoms. Cycle 17: After refmac, R = 0.1895 (Rfree = 0.000) for 10762 atoms. Found 140 (140 requested) and removed 106 (103 requested) atoms. Cycle 18: After refmac, R = 0.1811 (Rfree = 0.000) for 10790 atoms. Found 127 (137 requested) and removed 106 (103 requested) atoms. Cycle 19: After refmac, R = 0.1767 (Rfree = 0.000) for 10808 atoms. Found 100 (132 requested) and removed 107 (103 requested) atoms. Cycle 20: After refmac, R = 0.1756 (Rfree = 0.000) for 10790 atoms. Found 112 (128 requested) and removed 105 (103 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.50 2.57 NCS extension: 586 residues added (1374 deleted due to clashes), 11388 seeds are put forward Round 1: 1210 peptides, 43 chains. Longest chain 110 peptides. Score 0.916 Round 2: 1225 peptides, 34 chains. Longest chain 173 peptides. Score 0.929 Round 3: 1211 peptides, 46 chains. Longest chain 81 peptides. Score 0.912 Round 4: 1208 peptides, 43 chains. Longest chain 98 peptides. Score 0.915 Round 5: 1207 peptides, 64 chains. Longest chain 72 peptides. Score 0.887 Taking the results from Round 2 Chains 38, Residues 1191, Estimated correctness of the model 98.9 % 25 chains (1106 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 189 A and 200 A Built loop between residues 96 C and 99 C Built loop between residues 292 C and 295 C Built loop between residues 307 C and 310 C Built loop between residues 57 B and 60 B Built loop between residues 132 B and 136 B Built loop between residues 145 B and 151 B Built loop between residues 165 B and 168 B Built loop between residues 189 B and 196 B Built loop between residues 211 B and 214 B Built loop between residues 263 B and 267 B Built loop between residues 291 B and 294 B Built loop between residues 325 B and 328 B Built loop between residues 229 D and 232 D Built loop between residues 323 D and 326 D 22 chains (1237 residues) following loop building 10 chains (1153 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11433 restraints for refining 10813 atoms. 1839 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2089 (Rfree = 0.000) for 10813 atoms. Found 124 (124 requested) and removed 130 (103 requested) atoms. Cycle 22: After refmac, R = 0.1903 (Rfree = 0.000) for 10789 atoms. Found 120 (120 requested) and removed 104 (103 requested) atoms. Cycle 23: After refmac, R = 0.1827 (Rfree = 0.000) for 10796 atoms. Found 116 (116 requested) and removed 104 (103 requested) atoms. Cycle 24: After refmac, R = 0.1788 (Rfree = 0.000) for 10806 atoms. Found 108 (112 requested) and removed 105 (103 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1746 (Rfree = 0.000) for 10806 atoms. Found 108 (108 requested) and removed 105 (103 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.49 2.56 NCS extension: 226 residues added (314 deleted due to clashes), 11050 seeds are put forward Round 1: 1203 peptides, 40 chains. Longest chain 127 peptides. Score 0.918 Round 2: 1228 peptides, 32 chains. Longest chain 177 peptides. Score 0.932 Round 3: 1220 peptides, 39 chains. Longest chain 115 peptides. Score 0.922 Round 4: 1214 peptides, 43 chains. Longest chain 104 peptides. Score 0.916 Round 5: 1200 peptides, 51 chains. Longest chain 78 peptides. Score 0.903 Taking the results from Round 2 Chains 41, Residues 1196, Estimated correctness of the model 99.0 % 26 chains (1138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 A and 99 A Built loop between residues 210 A and 214 A Built loop between residues 241 A and 245 A Built loop between residues 292 A and 295 A Built loop between residues 328 A and 334 A Built loop between residues 189 C and 197 C Built loop between residues 226 C and 229 C Built loop between residues 292 C and 295 C Built loop between residues 307 C and 310 C Built loop between residues 169 B and 172 B Built loop between residues 189 B and 200 B Built loop between residues 212 B and 220 B Built loop between residues 231 B and 235 B Built loop between residues 126 D and 133 D Built loop between residues 229 D and 232 D Built loop between residues 292 D and 295 D Built loop between residues 319 D and 322 D 18 chains (1248 residues) following loop building 9 chains (1205 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11381 restraints for refining 10942 atoms. 1538 conditional restraints added. Observations/parameters ratio is 1.20 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2078 (Rfree = 0.000) for 10942 atoms. Found 105 (105 requested) and removed 131 (105 requested) atoms. Cycle 27: After refmac, R = 0.1870 (Rfree = 0.000) for 10904 atoms. Found 104 (104 requested) and removed 109 (104 requested) atoms. Cycle 28: After refmac, R = 0.1796 (Rfree = 0.000) for 10899 atoms. Found 104 (104 requested) and removed 107 (104 requested) atoms. Cycle 29: After refmac, R = 0.1749 (Rfree = 0.000) for 10893 atoms. Found 104 (104 requested) and removed 106 (104 requested) atoms. Cycle 30: After refmac, R = 0.1712 (Rfree = 0.000) for 10885 atoms. Found 104 (104 requested) and removed 106 (104 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.49 2.56 NCS extension: 526 residues added (1252 deleted due to clashes), 11421 seeds are put forward Round 1: 1217 peptides, 38 chains. Longest chain 115 peptides. Score 0.923 Round 2: 1235 peptides, 33 chains. Longest chain 154 peptides. Score 0.932 Round 3: 1224 peptides, 42 chains. Longest chain 140 peptides. Score 0.919 Round 4: 1215 peptides, 45 chains. Longest chain 155 peptides. Score 0.914 Round 5: 1215 peptides, 51 chains. Longest chain 129 peptides. Score 0.906 Taking the results from Round 2 Chains 39, Residues 1202, Estimated correctness of the model 99.0 % 21 chains (1125 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 101 A Built loop between residues 122 A and 133 A Built loop between residues 129 C and 131 C Built loop between residues 141 C and 146 C Built loop between residues 188 C and 196 C Built loop between residues 292 C and 295 C Built loop between residues 321 C and 325 C Built loop between residues 170 B and 174 B Built loop between residues 213 B and 216 B Built loop between residues 229 B and 234 B Built loop between residues 159 D and 162 D Built loop between residues 292 D and 295 D 22 chains (1242 residues) following loop building 9 chains (1173 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11488 restraints for refining 10847 atoms. 1794 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2059 (Rfree = 0.000) for 10847 atoms. Found 104 (104 requested) and removed 134 (104 requested) atoms. Cycle 32: After refmac, R = 0.1866 (Rfree = 0.000) for 10809 atoms. Found 103 (103 requested) and removed 104 (103 requested) atoms. Cycle 33: After refmac, R = 0.1790 (Rfree = 0.000) for 10803 atoms. Found 103 (103 requested) and removed 104 (103 requested) atoms. Cycle 34: After refmac, R = 0.1746 (Rfree = 0.000) for 10799 atoms. Found 103 (103 requested) and removed 108 (103 requested) atoms. Cycle 35: After refmac, R = 0.1722 (Rfree = 0.000) for 10789 atoms. Found 103 (103 requested) and removed 107 (103 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.50 2.57 NCS extension: 76 residues added (474 deleted due to clashes), 10883 seeds are put forward Round 1: 1196 peptides, 39 chains. Longest chain 111 peptides. Score 0.918 Round 2: 1213 peptides, 36 chains. Longest chain 135 peptides. Score 0.924 Round 3: 1213 peptides, 41 chains. Longest chain 104 peptides. Score 0.919 Round 4: 1206 peptides, 40 chains. Longest chain 120 peptides. Score 0.918 Round 5: 1183 peptides, 47 chains. Longest chain 74 peptides. Score 0.905 Taking the results from Round 2 Chains 39, Residues 1177, Estimated correctness of the model 98.8 % 25 chains (1114 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 133 A Built loop between residues 213 A and 216 A Built loop between residues 93 C and 96 C Built loop between residues 159 C and 162 C Built loop between residues 230 C and 233 C Built loop between residues 292 C and 295 C Built loop between residues 169 B and 173 B Built loop between residues 230 B and 233 B Built loop between residues 260 B and 263 B Built loop between residues 128 D and 131 D Built loop between residues 243 D and 246 D Built loop between residues 292 D and 295 D Built loop between residues 329 D and 334 D 25 chains (1211 residues) following loop building 12 chains (1151 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11609 restraints for refining 10740 atoms. 2100 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1977 (Rfree = 0.000) for 10740 atoms. Found 103 (103 requested) and removed 119 (103 requested) atoms. Cycle 37: After refmac, R = 0.1807 (Rfree = 0.000) for 10714 atoms. Found 103 (103 requested) and removed 103 (103 requested) atoms. Cycle 38: After refmac, R = 0.1735 (Rfree = 0.000) for 10710 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 39: After refmac, R = 0.1706 (Rfree = 0.000) for 10705 atoms. Found 102 (102 requested) and removed 106 (102 requested) atoms. Cycle 40: After refmac, R = 0.1684 (Rfree = 0.000) for 10697 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.49 2.56 NCS extension: 159 residues added (410 deleted due to clashes), 10870 seeds are put forward Round 1: 1193 peptides, 37 chains. Longest chain 117 peptides. Score 0.920 Round 2: 1220 peptides, 32 chains. Longest chain 133 peptides. Score 0.930 Round 3: 1193 peptides, 47 chains. Longest chain 116 peptides. Score 0.907 Round 4: 1184 peptides, 42 chains. Longest chain 110 peptides. Score 0.912 Round 5: 1168 peptides, 53 chains. Longest chain 74 peptides. Score 0.893 Taking the results from Round 2 Chains 38, Residues 1188, Estimated correctness of the model 99.0 % 24 chains (1104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 A and 216 A Built loop between residues 121 C and 124 C Built loop between residues 177 C and 180 C Built loop between residues 188 C and 196 C Built loop between residues 292 C and 295 C Built loop between residues 323 C and 326 C Built loop between residues 46 B and 49 B Built loop between residues 74 B and 77 B Built loop between residues 122 B and 133 B Built loop between residues 226 B and 229 B Built loop between residues 145 D and 148 D Built loop between residues 167 D and 170 D Built loop between residues 229 D and 232 D Built loop between residues 291 D and 294 D Built loop between residues 307 D and 310 D 21 chains (1227 residues) following loop building 9 chains (1147 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11296 restraints for refining 10693 atoms. 1752 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 10693 atoms. Found 102 (102 requested) and removed 116 (102 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 10665 atoms. Found 102 (102 requested) and removed 102 (102 requested) atoms. Cycle 43: After refmac, R = 0.1780 (Rfree = 0.000) for 10662 atoms. Found 102 (102 requested) and removed 106 (102 requested) atoms. Cycle 44: After refmac, R = 0.1738 (Rfree = 0.000) for 10655 atoms. Found 102 (102 requested) and removed 105 (102 requested) atoms. Cycle 45: After refmac, R = 0.1717 (Rfree = 0.000) for 10650 atoms. Found 102 (102 requested) and removed 107 (102 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.50 2.57 NCS extension: 479 residues added (761 deleted due to clashes), 11142 seeds are put forward Round 1: 1187 peptides, 35 chains. Longest chain 124 peptides. Score 0.921 Round 2: 1200 peptides, 31 chains. Longest chain 152 peptides. Score 0.928 Round 3: 1193 peptides, 40 chains. Longest chain 117 peptides. Score 0.916 Round 4: 1188 peptides, 47 chains. Longest chain 113 peptides. Score 0.906 Round 5: 1173 peptides, 44 chains. Longest chain 109 peptides. Score 0.907 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 1169, Estimated correctness of the model 98.9 % 23 chains (1097 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 169 A and 178 A Built loop between residues 190 A and 201 A Built loop between residues 212 A and 216 A Built loop between residues 108 C and 111 C Built loop between residues 127 C and 130 C Built loop between residues 190 C and 200 C Built loop between residues 94 B and 101 B Built loop between residues 127 B and 133 B Built loop between residues 185 B and 198 B Built loop between residues 292 B and 295 B Built loop between residues 70 D and 73 D Built loop between residues 97 D and 100 D Built loop between residues 159 D and 162 D Built loop between residues 188 D and 195 D Built loop between residues 243 D and 246 D Built loop between residues 292 D and 295 D Built loop between residues 323 D and 330 D 15 chains (1249 residues) following loop building 6 chains (1178 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 52490 reflections ( 98.47 % complete ) and 9748 restraints for refining 9552 atoms. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2683 (Rfree = 0.000) for 9552 atoms. Found 68 (91 requested) and removed 0 (91 requested) atoms. Cycle 47: After refmac, R = 0.2501 (Rfree = 0.000) for 9552 atoms. Found 43 (92 requested) and removed 5 (92 requested) atoms. Cycle 48: After refmac, R = 0.2425 (Rfree = 0.000) for 9552 atoms. Found 32 (92 requested) and removed 5 (92 requested) atoms. Cycle 49: After refmac, R = 0.2380 (Rfree = 0.000) for 9552 atoms. Found 19 (93 requested) and removed 10 (93 requested) atoms. Writing output files ... TimeTaking 160.05