null Mon 24 Dec 00:44:16 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 1vkn-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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/1vkn-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:44:20 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/1vkn-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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 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-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-2.5-parrot-mrncs.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 12364 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Starting model: R = 0.3067 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2094 (Rfree = 0.000) for 12364 atoms. Found 221 (237 requested) and removed 133 (118 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.46 2.53 NCS extension: 0 residues added, 12452 seeds are put forward Round 1: 869 peptides, 126 chains. Longest chain 23 peptides. Score 0.563 Round 2: 994 peptides, 80 chains. Longest chain 50 peptides. Score 0.784 Round 3: 1075 peptides, 75 chains. Longest chain 51 peptides. Score 0.829 Round 4: 1108 peptides, 63 chains. Longest chain 63 peptides. Score 0.862 Round 5: 1114 peptides, 60 chains. Longest chain 80 peptides. Score 0.869 Taking the results from Round 5 Chains 62, Residues 1054, Estimated correctness of the model 96.7 % 31 chains (860 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 177 A Built loop between residues 230 A and 234 A Built loop between residues 68 C and 71 C Built loop between residues 122 C and 129 C Built loop between residues 244 C and 247 C Built loop between residues 282 C and 288 C Built loop between residues 308 C and 311 C Built loop between residues 91 D and 99 D Built loop between residues 127 D and 131 D Built loop between residues 168 D and 172 D Built loop between residues 189 D and 197 D Built loop between residues 257 D and 265 D Built loop between residues 292 D and 295 D Built loop between residues 305 D and 311 D Built loop between residues 323 D and 329 D 45 chains (1115 residues) following loop building 16 chains (928 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 13260 restraints for refining 10771 atoms. 5083 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2539 (Rfree = 0.000) for 10771 atoms. Found 207 (207 requested) and removed 147 (103 requested) atoms. Cycle 2: After refmac, R = 0.2190 (Rfree = 0.000) for 10749 atoms. Found 173 (204 requested) and removed 109 (104 requested) atoms. Cycle 3: After refmac, R = 0.2035 (Rfree = 0.000) for 10766 atoms. Found 134 (199 requested) and removed 105 (103 requested) atoms. Cycle 4: After refmac, R = 0.1946 (Rfree = 0.000) for 10761 atoms. Found 117 (195 requested) and removed 111 (103 requested) atoms. Cycle 5: After refmac, R = 0.1915 (Rfree = 0.000) for 10745 atoms. Found 98 (190 requested) and removed 109 (103 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.48 2.55 NCS extension: 429 residues added (889 deleted due to clashes), 11193 seeds are put forward Round 1: 1125 peptides, 60 chains. Longest chain 111 peptides. Score 0.872 Round 2: 1138 peptides, 41 chains. Longest chain 151 peptides. Score 0.903 Round 3: 1148 peptides, 43 chains. Longest chain 75 peptides. Score 0.903 Round 4: 1127 peptides, 53 chains. Longest chain 81 peptides. Score 0.883 Round 5: 1161 peptides, 45 chains. Longest chain 98 peptides. Score 0.903 Taking the results from Round 5 Chains 51, Residues 1116, Estimated correctness of the model 98.1 % 28 chains (983 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 261 A and 265 A Built loop between residues 174 C and 179 C Built loop between residues 215 C and 219 C Built loop between residues 292 C and 295 C Built loop between residues 319 C and 322 C Built loop between residues 327 C and 330 C Built loop between residues 170 B and 172 B Built loop between residues 265 B and 269 B Built loop between residues 292 D and 295 D Built loop between residues 307 D and 310 D 40 chains (1139 residues) following loop building 18 chains (1007 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 12336 restraints for refining 10553 atoms. 3742 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2164 (Rfree = 0.000) for 10553 atoms. Found 182 (182 requested) and removed 113 (101 requested) atoms. Cycle 7: After refmac, R = 0.1962 (Rfree = 0.000) for 10592 atoms. Found 136 (180 requested) and removed 103 (102 requested) atoms. Cycle 8: After refmac, R = 0.1866 (Rfree = 0.000) for 10601 atoms. Found 114 (175 requested) and removed 105 (102 requested) atoms. Cycle 9: After refmac, R = 0.1814 (Rfree = 0.000) for 10598 atoms. Found 123 (171 requested) and removed 103 (101 requested) atoms. Cycle 10: After refmac, R = 0.1782 (Rfree = 0.000) for 10616 atoms. Found 112 (166 requested) and removed 103 (101 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.50 2.57 NCS extension: 149 residues added (430 deleted due to clashes), 10794 seeds are put forward Round 1: 1129 peptides, 46 chains. Longest chain 104 peptides. Score 0.894 Round 2: 1171 peptides, 31 chains. Longest chain 175 peptides. Score 0.923 Round 3: 1165 peptides, 43 chains. Longest chain 108 peptides. Score 0.907 Round 4: 1139 peptides, 49 chains. Longest chain 79 peptides. Score 0.892 Round 5: 1141 peptides, 53 chains. Longest chain 96 peptides. Score 0.887 Taking the results from Round 2 Chains 36, Residues 1140, Estimated correctness of the model 98.8 % 19 chains (1021 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 291 A and 294 A Built loop between residues 229 C and 232 C Built loop between residues 292 C and 295 C Built loop between residues 62 B and 64 B Built loop between residues 87 B and 98 B Built loop between residues 126 B and 132 B Built loop between residues 189 B and 200 B Built loop between residues 190 D and 200 D Built loop between residues 289 D and 295 D 24 chains (1179 residues) following loop building 10 chains (1067 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11904 restraints for refining 10598 atoms. 2897 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2072 (Rfree = 0.000) for 10598 atoms. Found 162 (162 requested) and removed 117 (101 requested) atoms. Cycle 12: After refmac, R = 0.1894 (Rfree = 0.000) for 10634 atoms. Found 147 (159 requested) and removed 103 (102 requested) atoms. Cycle 13: After refmac, R = 0.1793 (Rfree = 0.000) for 10673 atoms. Found 110 (156 requested) and removed 104 (102 requested) atoms. Cycle 14: After refmac, R = 0.1747 (Rfree = 0.000) for 10673 atoms. Found 100 (152 requested) and removed 105 (102 requested) atoms. Cycle 15: After refmac, R = 0.1729 (Rfree = 0.000) for 10667 atoms. Found 114 (147 requested) and removed 104 (102 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.51 2.58 NCS extension: 456 residues added (624 deleted due to clashes), 11157 seeds are put forward Round 1: 1177 peptides, 38 chains. Longest chain 115 peptides. Score 0.915 Round 2: 1193 peptides, 31 chains. Longest chain 122 peptides. Score 0.927 Round 3: 1176 peptides, 36 chains. Longest chain 112 peptides. Score 0.918 Round 4: 1188 peptides, 47 chains. Longest chain 97 peptides. Score 0.906 Round 5: 1175 peptides, 44 chains. Longest chain 92 peptides. Score 0.907 Taking the results from Round 2 Chains 38, Residues 1162, Estimated correctness of the model 98.9 % 23 chains (1081 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 28 A Built loop between residues 48 A and 51 A Built loop between residues 292 A and 295 A Built loop between residues 61 C and 64 C Built loop between residues 90 C and 98 C Built loop between residues 159 C and 162 C Built loop between residues 229 C and 232 C Built loop between residues 68 B and 71 B Built loop between residues 191 B and 198 B Built loop between residues 292 B and 295 B Built loop between residues 332 B and 335 B Built loop between residues 259 D and 263 D 24 chains (1194 residues) following loop building 11 chains (1115 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11412 restraints for refining 10571 atoms. 2151 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2040 (Rfree = 0.000) for 10571 atoms. Found 142 (142 requested) and removed 118 (101 requested) atoms. Cycle 17: After refmac, R = 0.1877 (Rfree = 0.000) for 10581 atoms. Found 138 (138 requested) and removed 104 (101 requested) atoms. Cycle 18: After refmac, R = 0.1808 (Rfree = 0.000) for 10611 atoms. Found 132 (134 requested) and removed 104 (101 requested) atoms. Cycle 19: After refmac, R = 0.1766 (Rfree = 0.000) for 10635 atoms. Found 128 (131 requested) and removed 106 (102 requested) atoms. Cycle 20: After refmac, R = 0.1734 (Rfree = 0.000) for 10653 atoms. Found 126 (126 requested) and removed 108 (102 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.50 2.57 NCS extension: 173 residues added (398 deleted due to clashes), 10855 seeds are put forward Round 1: 1178 peptides, 33 chains. Longest chain 127 peptides. Score 0.922 Round 2: 1190 peptides, 33 chains. Longest chain 179 peptides. Score 0.924 Round 3: 1177 peptides, 43 chains. Longest chain 97 peptides. Score 0.909 Round 4: 1189 peptides, 41 chains. Longest chain 101 peptides. Score 0.914 Round 5: 1174 peptides, 51 chains. Longest chain 96 peptides. Score 0.898 Taking the results from Round 2 Chains 42, Residues 1157, Estimated correctness of the model 98.8 % 26 chains (1078 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 28 A Built loop between residues 166 C and 169 C Built loop between residues 228 C and 231 C Built loop between residues 28 B and 32 B Built loop between residues 256 B and 260 B Built loop between residues 292 B and 295 B Built loop between residues 317 B and 321 B Built loop between residues 190 D and 197 D Built loop between residues 258 D and 261 D Built loop between residues 292 D and 295 D Built loop between residues 307 D and 310 D 30 chains (1185 residues) following loop building 15 chains (1107 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11772 restraints for refining 10626 atoms. 2609 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1994 (Rfree = 0.000) for 10626 atoms. Found 122 (122 requested) and removed 114 (102 requested) atoms. Cycle 22: After refmac, R = 0.1845 (Rfree = 0.000) for 10628 atoms. Found 118 (118 requested) and removed 103 (102 requested) atoms. Cycle 23: After refmac, R = 0.1788 (Rfree = 0.000) for 10641 atoms. Found 114 (114 requested) and removed 102 (102 requested) atoms. Cycle 24: After refmac, R = 0.1749 (Rfree = 0.000) for 10649 atoms. Found 110 (110 requested) and removed 105 (102 requested) atoms. Cycle 25: After refmac, R = 0.1727 (Rfree = 0.000) for 10652 atoms. Found 105 (106 requested) and removed 104 (102 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.50 2.57 NCS extension: 220 residues added (983 deleted due to clashes), 10884 seeds are put forward Round 1: 1178 peptides, 38 chains. Longest chain 134 peptides. Score 0.916 Round 2: 1196 peptides, 34 chains. Longest chain 118 peptides. Score 0.924 Round 3: 1186 peptides, 39 chains. Longest chain 76 peptides. Score 0.916 Round 4: 1179 peptides, 48 chains. Longest chain 116 peptides. Score 0.903 Round 5: 1173 peptides, 52 chains. Longest chain 112 peptides. Score 0.896 Taking the results from Round 2 Chains 38, Residues 1162, Estimated correctness of the model 98.8 % 27 chains (1083 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 28 A Built loop between residues 127 A and 135 A Built loop between residues 174 A and 177 A Built loop between residues 294 A and 297 A Built loop between residues 170 C and 174 C Built loop between residues 189 C and 200 C Built loop between residues 260 C and 263 C Built loop between residues 61 B and 64 B Built loop between residues 91 B and 99 B Built loop between residues 141 B and 144 B Built loop between residues 229 B and 232 B Built loop between residues 292 B and 295 B Built loop between residues 191 D and 198 D Built loop between residues 242 D and 245 D Built loop between residues 292 D and 295 D Built loop between residues 307 D and 310 D Built loop between residues 327 D and 330 D 20 chains (1217 residues) following loop building 10 chains (1140 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11524 restraints for refining 10718 atoms. 2063 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2042 (Rfree = 0.000) for 10718 atoms. Found 102 (102 requested) and removed 123 (102 requested) atoms. Cycle 27: After refmac, R = 0.1863 (Rfree = 0.000) for 10689 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 28: After refmac, R = 0.1794 (Rfree = 0.000) for 10683 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 29: After refmac, R = 0.1756 (Rfree = 0.000) for 10678 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 30: After refmac, R = 0.1734 (Rfree = 0.000) for 10675 atoms. Found 102 (102 requested) and removed 105 (102 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.50 2.57 NCS extension: 96 residues added (441 deleted due to clashes), 10784 seeds are put forward Round 1: 1188 peptides, 40 chains. Longest chain 109 peptides. Score 0.915 Round 2: 1189 peptides, 42 chains. Longest chain 119 peptides. Score 0.913 Round 3: 1175 peptides, 47 chains. Longest chain 115 peptides. Score 0.903 Round 4: 1181 peptides, 48 chains. Longest chain 75 peptides. Score 0.903 Round 5: 1173 peptides, 55 chains. Longest chain 69 peptides. Score 0.892 Taking the results from Round 1 Chains 43, Residues 1148, Estimated correctness of the model 98.5 % 29 chains (1076 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 133 A Built loop between residues 74 C and 77 C Built loop between residues 128 C and 136 C Built loop between residues 191 C and 198 C Built loop between residues 292 C and 295 C Built loop between residues 332 C and 335 C Built loop between residues 26 B and 28 B Built loop between residues 48 B and 52 B Built loop between residues 169 B and 172 B Built loop between residues 260 B and 264 B Built loop between residues 280 B and 283 B Built loop between residues 93 D and 100 D Built loop between residues 167 D and 170 D Built loop between residues 229 D and 232 D Built loop between residues 274 D and 277 D Built loop between residues 292 D and 295 D Built loop between residues 308 D and 311 D Built loop between residues 322 D and 326 D 23 chains (1198 residues) following loop building 11 chains (1130 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11648 restraints for refining 10699 atoms. 2265 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1994 (Rfree = 0.000) for 10699 atoms. Found 102 (102 requested) and removed 114 (102 requested) atoms. Cycle 32: After refmac, R = 0.1841 (Rfree = 0.000) for 10678 atoms. Found 102 (102 requested) and removed 102 (102 requested) atoms. Cycle 33: After refmac, R = 0.1788 (Rfree = 0.000) for 10672 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 34: After refmac, R = 0.1768 (Rfree = 0.000) for 10667 atoms. Found 102 (102 requested) and removed 109 (102 requested) atoms. Cycle 35: After refmac, R = 0.1729 (Rfree = 0.000) for 10660 atoms. Found 102 (102 requested) and removed 108 (102 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.48 2.55 NCS extension: 147 residues added (410 deleted due to clashes), 10818 seeds are put forward Round 1: 1175 peptides, 41 chains. Longest chain 115 peptides. Score 0.911 Round 2: 1191 peptides, 40 chains. Longest chain 107 peptides. Score 0.916 Round 3: 1186 peptides, 41 chains. Longest chain 121 peptides. Score 0.913 Round 4: 1172 peptides, 51 chains. Longest chain 112 peptides. Score 0.897 Round 5: 1189 peptides, 46 chains. Longest chain 125 peptides. Score 0.908 Taking the results from Round 2 Chains 48, Residues 1151, Estimated correctness of the model 98.5 % 28 chains (1043 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 35 A Built loop between residues 323 A and 328 A Built loop between residues 245 C and 248 C Built loop between residues 262 C and 272 C Built loop between residues 61 B and 64 B Built loop between residues 93 B and 99 B Built loop between residues 212 B and 215 B Built loop between residues 288 B and 295 B Built loop between residues 307 B and 310 B Built loop between residues 126 D and 131 D Built loop between residues 141 D and 144 D Built loop between residues 191 D and 199 D Built loop between residues 243 D and 246 D Built loop between residues 308 D and 311 D 29 chains (1193 residues) following loop building 14 chains (1100 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11847 restraints for refining 10679 atoms. 2656 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2051 (Rfree = 0.000) for 10679 atoms. Found 102 (102 requested) and removed 121 (102 requested) atoms. Cycle 37: After refmac, R = 0.1871 (Rfree = 0.000) for 10652 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 38: After refmac, R = 0.1801 (Rfree = 0.000) for 10646 atoms. Found 102 (102 requested) and removed 103 (102 requested) atoms. Cycle 39: After refmac, R = 0.1752 (Rfree = 0.000) for 10643 atoms. Found 102 (102 requested) and removed 109 (102 requested) atoms. Cycle 40: After refmac, R = 0.1729 (Rfree = 0.000) for 10633 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.49 2.56 NCS extension: 157 residues added (397 deleted due to clashes), 10815 seeds are put forward Round 1: 1162 peptides, 38 chains. Longest chain 125 peptides. Score 0.912 Round 2: 1189 peptides, 39 chains. Longest chain 93 peptides. Score 0.917 Round 3: 1183 peptides, 36 chains. Longest chain 116 peptides. Score 0.919 Round 4: 1178 peptides, 44 chains. Longest chain 116 peptides. Score 0.908 Round 5: 1186 peptides, 44 chains. Longest chain 114 peptides. Score 0.910 Taking the results from Round 3 Chains 41, Residues 1147, Estimated correctness of the model 98.6 % 30 chains (1107 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 71 A and 74 A Built loop between residues 93 A and 99 A Built loop between residues 141 A and 144 A Built loop between residues 269 A and 272 A Built loop between residues 308 A and 311 A Built loop between residues 330 A and 333 A Built loop between residues 189 C and 200 C Built loop between residues 291 C and 294 C Built loop between residues 26 B and 28 B Built loop between residues 45 B and 52 B Built loop between residues 122 B and 133 B Built loop between residues 229 B and 232 B Built loop between residues 290 B and 295 B Built loop between residues 323 B and 328 B Built loop between residues 128 D and 131 D Built loop between residues 166 D and 169 D Built loop between residues 191 D and 198 D Built loop between residues 308 D and 311 D Built loop between residues 323 D and 327 D 18 chains (1211 residues) following loop building 10 chains (1178 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11407 restraints for refining 10892 atoms. 1781 conditional restraints added. Observations/parameters ratio is 1.20 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2096 (Rfree = 0.000) for 10892 atoms. Found 104 (104 requested) and removed 152 (104 requested) atoms. Cycle 42: After refmac, R = 0.1895 (Rfree = 0.000) for 10827 atoms. Found 104 (104 requested) and removed 106 (104 requested) atoms. Cycle 43: After refmac, R = 0.1815 (Rfree = 0.000) for 10814 atoms. Found 103 (103 requested) and removed 105 (103 requested) atoms. Cycle 44: After refmac, R = 0.1773 (Rfree = 0.000) for 10808 atoms. Found 103 (103 requested) and removed 105 (103 requested) atoms. Cycle 45: After refmac, R = 0.1738 (Rfree = 0.000) for 10801 atoms. Found 103 (103 requested) and removed 110 (103 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.49 2.56 NCS extension: 117 residues added (166 deleted due to clashes), 10927 seeds are put forward Round 1: 1190 peptides, 33 chains. Longest chain 118 peptides. Score 0.924 Round 2: 1193 peptides, 35 chains. Longest chain 109 peptides. Score 0.922 Round 3: 1172 peptides, 43 chains. Longest chain 103 peptides. Score 0.908 Round 4: 1173 peptides, 48 chains. Longest chain 107 peptides. Score 0.902 Round 5: 1178 peptides, 48 chains. Longest chain 73 peptides. Score 0.903 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 1157, Estimated correctness of the model 98.8 % 23 chains (1087 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 48 A and 52 A Built loop between residues 121 A and 133 A Built loop between residues 308 A and 311 A Built loop between residues 322 A and 325 A Built loop between residues 88 C and 99 C Built loop between residues 189 C and 197 C Built loop between residues 292 C and 295 C Built loop between residues 323 C and 334 C Built loop between residues 189 B and 200 B Built loop between residues 129 D and 136 D Built loop between residues 230 D and 233 D Built loop between residues 290 D and 294 D Built loop between residues 308 D and 311 D Built loop between residues 320 D and 325 D 18 chains (1218 residues) following loop building 9 chains (1161 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 52490 reflections ( 98.47 % complete ) and 9576 restraints for refining 9383 atoms. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2654 (Rfree = 0.000) for 9383 atoms. Found 69 (90 requested) and removed 0 (90 requested) atoms. Cycle 47: After refmac, R = 0.2468 (Rfree = 0.000) for 9383 atoms. Found 39 (90 requested) and removed 6 (90 requested) atoms. Cycle 48: After refmac, R = 0.2397 (Rfree = 0.000) for 9383 atoms. Found 21 (91 requested) and removed 7 (91 requested) atoms. Cycle 49: After refmac, R = 0.2363 (Rfree = 0.000) for 9383 atoms. Found 18 (91 requested) and removed 8 (91 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:04:45 GMT 2018 Job finished. TimeTaking 140.5 Used memory is bytes: 22237712