Mon 24 Dec 00:57:12 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 2anu-2.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-2.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-2.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-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/2anu-2.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-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 00:57:16 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/2anu-2.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-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 1653 and 0 Target number of residues in the AU: 1653 Target solvent content: 0.5101 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-2.3-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-2.3-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.70 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: 127.729 2.300 Wilson plot Bfac: 25.60 78583 reflections ( 99.94 % complete ) and 0 restraints for refining 13645 atoms. Observations/parameters ratio is 1.44 ------------------------------------------------------ Starting model: R = 0.2829 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1997 (Rfree = 0.000) for 13645 atoms. Found 313 (313 requested) and removed 165 (156 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.20 2.06 NCS extension: 0 residues added, 13793 seeds are put forward Round 1: 1042 peptides, 128 chains. Longest chain 30 peptides. Score 0.621 Round 2: 1186 peptides, 82 chains. Longest chain 74 peptides. Score 0.798 Round 3: 1235 peptides, 57 chains. Longest chain 83 peptides. Score 0.856 Round 4: 1258 peptides, 47 chains. Longest chain 82 peptides. Score 0.876 Round 5: 1279 peptides, 51 chains. Longest chain 83 peptides. Score 0.875 Taking the results from Round 4 Chains 52, Residues 1211, Estimated correctness of the model 97.6 % 32 chains (1084 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 73 A Built loop between residues 138 A and 142 A Built loop between residues 154 A and 164 A Built loop between residues 67 C and 74 C Built loop between residues 185 C and 188 C Built loop between residues 144 B and 147 B Built loop between residues 182 B and 187 B Built loop between residues 203 B and 206 B Built loop between residues 98 E and 109 E Built loop between residues 129 E and 135 E Built loop between residues 155 E and 164 E Built loop between residues 178 E and 181 E Built loop between residues 191 E and 195 E Built loop between residues 212 E and 221 E Built loop between residues 67 D and 71 D Built loop between residues 80 D and 86 D Built loop between residues 195 D and 198 D Built loop between residues 83 F and 86 F 29 chains (1280 residues) following loop building 14 chains (1166 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 14279 restraints for refining 12661 atoms. 3909 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2221 (Rfree = 0.000) for 12661 atoms. Found 291 (291 requested) and removed 187 (145 requested) atoms. Cycle 2: After refmac, R = 0.1976 (Rfree = 0.000) for 12656 atoms. Found 268 (287 requested) and removed 162 (146 requested) atoms. Cycle 3: After refmac, R = 0.1871 (Rfree = 0.000) for 12695 atoms. Found 230 (281 requested) and removed 165 (146 requested) atoms. Cycle 4: After refmac, R = 0.1816 (Rfree = 0.000) for 12719 atoms. Found 200 (275 requested) and removed 163 (146 requested) atoms. Cycle 5: After refmac, R = 0.1765 (Rfree = 0.000) for 12724 atoms. Found 200 (270 requested) and removed 168 (146 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.17 2.03 NCS extension: 147 residues added (1399 deleted due to clashes), 12923 seeds are put forward Round 1: 1306 peptides, 32 chains. Longest chain 139 peptides. Score 0.905 Round 2: 1303 peptides, 35 chains. Longest chain 140 peptides. Score 0.901 Round 3: 1306 peptides, 27 chains. Longest chain 140 peptides. Score 0.911 Round 4: 1306 peptides, 35 chains. Longest chain 140 peptides. Score 0.902 Round 5: 1307 peptides, 30 chains. Longest chain 141 peptides. Score 0.908 Taking the results from Round 3 Chains 29, Residues 1279, Estimated correctness of the model 98.7 % 25 chains (1215 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 164 A Built loop between residues 170 A and 173 A Built loop between residues 203 A and 206 A Built loop between residues 155 C and 164 C Built loop between residues 204 C and 207 C Built loop between residues 38 B and 43 B Built loop between residues 68 B and 71 B Built loop between residues 84 B and 87 B Built loop between residues 156 B and 165 B Built loop between residues 204 B and 207 B Built loop between residues 67 E and 70 E Built loop between residues 188 E and 192 E Built loop between residues 156 D and 164 D Built loop between residues 66 F and 73 F Built loop between residues 204 F and 207 F 12 chains (1337 residues) following loop building 10 chains (1275 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 13120 restraints for refining 12475 atoms. 1933 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1992 (Rfree = 0.000) for 12475 atoms. Found 257 (257 requested) and removed 174 (143 requested) atoms. Cycle 7: After refmac, R = 0.1758 (Rfree = 0.000) for 12527 atoms. Found 253 (253 requested) and removed 153 (144 requested) atoms. Cycle 8: After refmac, R = 0.1669 (Rfree = 0.000) for 12617 atoms. Found 249 (249 requested) and removed 164 (145 requested) atoms. Cycle 9: After refmac, R = 0.1607 (Rfree = 0.000) for 12691 atoms. Found 245 (245 requested) and removed 163 (146 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1580 (Rfree = 0.000) for 12757 atoms. Found 240 (240 requested) and removed 171 (146 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.16 2.02 NCS extension: 30 residues added (701 deleted due to clashes), 12874 seeds are put forward Round 1: 1311 peptides, 27 chains. Longest chain 140 peptides. Score 0.912 Round 2: 1307 peptides, 28 chains. Longest chain 140 peptides. Score 0.910 Round 3: 1315 peptides, 26 chains. Longest chain 140 peptides. Score 0.914 Round 4: 1310 peptides, 31 chains. Longest chain 140 peptides. Score 0.907 Round 5: 1300 peptides, 35 chains. Longest chain 139 peptides. Score 0.901 Taking the results from Round 3 Chains 27, Residues 1289, Estimated correctness of the model 98.8 % 24 chains (1275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 164 A Built loop between residues 84 C and 87 C Built loop between residues 177 C and 180 C Built loop between residues 194 C and 197 C Built loop between residues 203 C and 206 C Built loop between residues 156 B and 165 B Built loop between residues 203 B and 206 B Built loop between residues 67 E and 70 E Built loop between residues 155 E and 163 E Built loop between residues 204 E and 207 E Built loop between residues 122 D and 125 D Built loop between residues 156 D and 164 D Built loop between residues 204 D and 207 D Built loop between residues 155 F and 165 F Built loop between residues 204 F and 207 F Built loop between residues 219 F and 222 F 10 chains (1348 residues) following loop building 8 chains (1336 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12622 restraints for refining 12457 atoms. 1135 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1849 (Rfree = 0.000) for 12457 atoms. Found 229 (229 requested) and removed 163 (143 requested) atoms. Cycle 12: After refmac, R = 0.1683 (Rfree = 0.000) for 12507 atoms. Found 225 (225 requested) and removed 149 (144 requested) atoms. Cycle 13: After refmac, R = 0.1620 (Rfree = 0.000) for 12572 atoms. Found 220 (220 requested) and removed 158 (144 requested) atoms. Cycle 14: After refmac, R = 0.1584 (Rfree = 0.000) for 12625 atoms. Found 215 (215 requested) and removed 160 (145 requested) atoms. Cycle 15: After refmac, R = 0.1557 (Rfree = 0.000) for 12669 atoms. Found 210 (210 requested) and removed 168 (145 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.15 2.01 NCS extension: 15 residues added (190 deleted due to clashes), 12737 seeds are put forward Round 1: 1324 peptides, 23 chains. Longest chain 141 peptides. Score 0.919 Round 2: 1307 peptides, 28 chains. Longest chain 140 peptides. Score 0.910 Round 3: 1313 peptides, 30 chains. Longest chain 141 peptides. Score 0.909 Round 4: 1305 peptides, 33 chains. Longest chain 139 peptides. Score 0.904 Round 5: 1309 peptides, 32 chains. Longest chain 139 peptides. Score 0.906 Taking the results from Round 1 Chains 24, Residues 1301, Estimated correctness of the model 98.9 % 23 chains (1300 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A Built loop between residues 156 A and 164 A Built loop between residues 204 A and 207 A Built loop between residues 144 C and 147 C Built loop between residues 155 C and 165 C Built loop between residues 204 C and 207 C Built loop between residues 157 B and 163 B Built loop between residues 204 B and 207 B Built loop between residues 40 E and 43 E Built loop between residues 156 E and 163 E Built loop between residues 204 E and 207 E Built loop between residues 99 D and 102 D Built loop between residues 155 D and 164 D Built loop between residues 190 D and 193 D Built loop between residues 203 D and 206 D Built loop between residues 155 F and 164 F Built loop between residues 204 F and 207 F 6 chains (1365 residues) following loop building 6 chains (1365 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 78583 reflections ( 99.94 % complete ) and 12463 restraints for refining 12493 atoms. 778 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1772 (Rfree = 0.000) for 12493 atoms. Found 201 (201 requested) and removed 165 (143 requested) atoms. Cycle 17: After refmac, R = 0.1624 (Rfree = 0.000) for 12517 atoms. Found 196 (196 requested) and removed 146 (144 requested) atoms. Cycle 18: After refmac, R = 0.1575 (Rfree = 0.000) for 12560 atoms. Found 191 (191 requested) and removed 154 (144 requested) atoms. Cycle 19: After refmac, R = 0.1554 (Rfree = 0.000) for 12587 atoms. Found 185 (185 requested) and removed 159 (144 requested) atoms. Cycle 20: After refmac, R = 0.1553 (Rfree = 0.000) for 12606 atoms. Found 180 (180 requested) and removed 166 (145 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.15 2.01 NCS extension: 6 residues added (169 deleted due to clashes), 12640 seeds are put forward Round 1: 1314 peptides, 27 chains. Longest chain 139 peptides. Score 0.913 Round 2: 1318 peptides, 28 chains. Longest chain 139 peptides. Score 0.912 Round 3: 1322 peptides, 29 chains. Longest chain 142 peptides. Score 0.912 Round 4: 1309 peptides, 34 chains. Longest chain 121 peptides. Score 0.904 Round 5: 1318 peptides, 30 chains. Longest chain 142 peptides. Score 0.910 Taking the results from Round 1 Chains 29, Residues 1287, Estimated correctness of the model 98.7 % 27 chains (1285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A Built loop between residues 156 A and 163 A Built loop between residues 186 A and 192 A Built loop between residues 203 A and 206 A Built loop between residues 83 C and 86 C Built loop between residues 156 C and 164 C Built loop between residues 185 C and 192 C Built loop between residues 43 B and 46 B Built loop between residues 83 B and 86 B Built loop between residues 157 B and 164 B Built loop between residues 185 B and 188 B Built loop between residues 203 B and 206 B Built loop between residues 81 E and 85 E Built loop between residues 155 E and 165 E Built loop between residues 204 E and 207 E Built loop between residues 155 D and 162 D Built loop between residues 204 D and 207 D Built loop between residues 155 F and 164 F Built loop between residues 185 F and 188 F 8 chains (1361 residues) following loop building 8 chains (1361 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12516 restraints for refining 12442 atoms. 861 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1770 (Rfree = 0.000) for 12442 atoms. Found 172 (172 requested) and removed 158 (143 requested) atoms. Cycle 22: After refmac, R = 0.1632 (Rfree = 0.000) for 12444 atoms. Found 166 (166 requested) and removed 144 (143 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1587 (Rfree = 0.000) for 12457 atoms. Found 160 (160 requested) and removed 151 (143 requested) atoms. Cycle 24: After refmac, R = 0.1555 (Rfree = 0.000) for 12461 atoms. Found 154 (154 requested) and removed 153 (143 requested) atoms. Cycle 25: After refmac, R = 0.1529 (Rfree = 0.000) for 12459 atoms. Found 149 (149 requested) and removed 145 (143 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.15 2.01 NCS extension: 9 residues added (346 deleted due to clashes), 12478 seeds are put forward Round 1: 1317 peptides, 28 chains. Longest chain 139 peptides. Score 0.912 Round 2: 1322 peptides, 29 chains. Longest chain 142 peptides. Score 0.912 Round 3: 1322 peptides, 32 chains. Longest chain 142 peptides. Score 0.908 Round 4: 1315 peptides, 33 chains. Longest chain 139 peptides. Score 0.906 Round 5: 1317 peptides, 33 chains. Longest chain 93 peptides. Score 0.906 Taking the results from Round 2 Chains 29, Residues 1293, Estimated correctness of the model 98.7 % 28 chains (1289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 161 A Built loop between residues 177 A and 180 A Built loop between residues 203 A and 206 A Built loop between residues 61 C and 65 C Built loop between residues 156 C and 164 C Built loop between residues 186 C and 188 C Built loop between residues 203 C and 206 C Built loop between residues 84 B and 87 B Built loop between residues 144 B and 147 B Built loop between residues 157 B and 163 B Built loop between residues 204 B and 207 B Built loop between residues 61 E and 70 E Built loop between residues 156 E and 164 E Built loop between residues 190 E and 193 E Built loop between residues 203 E and 206 E Built loop between residues 158 D and 164 D Built loop between residues 189 D and 192 D Built loop between residues 84 F and 87 F Built loop between residues 122 F and 125 F Built loop between residues 155 F and 164 F Built loop between residues 204 F and 207 F 7 chains (1362 residues) following loop building 7 chains (1362 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12481 restraints for refining 12435 atoms. 820 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1806 (Rfree = 0.000) for 12435 atoms. Found 143 (143 requested) and removed 160 (143 requested) atoms. Cycle 27: After refmac, R = 0.1641 (Rfree = 0.000) for 12411 atoms. Found 142 (142 requested) and removed 143 (142 requested) atoms. Cycle 28: After refmac, R = 0.1584 (Rfree = 0.000) for 12402 atoms. Found 142 (142 requested) and removed 144 (142 requested) atoms. Cycle 29: After refmac, R = 0.1564 (Rfree = 0.000) for 12395 atoms. Found 142 (142 requested) and removed 149 (142 requested) atoms. Cycle 30: After refmac, R = 0.1553 (Rfree = 0.000) for 12383 atoms. Found 142 (142 requested) and removed 147 (142 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.16 2.02 NCS extension: 11 residues added (415 deleted due to clashes), 12402 seeds are put forward Round 1: 1321 peptides, 26 chains. Longest chain 140 peptides. Score 0.915 Round 2: 1317 peptides, 27 chains. Longest chain 140 peptides. Score 0.913 Round 3: 1312 peptides, 32 chains. Longest chain 140 peptides. Score 0.907 Round 4: 1309 peptides, 31 chains. Longest chain 139 peptides. Score 0.907 Round 5: 1310 peptides, 36 chains. Longest chain 91 peptides. Score 0.901 Taking the results from Round 1 Chains 29, Residues 1295, Estimated correctness of the model 98.8 % 26 chains (1292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 163 A Built loop between residues 185 A and 188 A Built loop between residues 203 A and 206 A Built loop between residues 83 C and 86 C Built loop between residues 156 C and 165 C Built loop between residues 185 C and 188 C Built loop between residues 203 C and 206 C Built loop between residues 144 B and 147 B Built loop between residues 156 B and 164 B Built loop between residues 204 B and 207 B Built loop between residues 83 E and 86 E Built loop between residues 156 E and 163 E Built loop between residues 186 E and 192 E Built loop between residues 203 E and 206 E Built loop between residues 83 D and 86 D Built loop between residues 156 D and 164 D Built loop between residues 204 D and 207 D Built loop between residues 156 F and 164 F Built loop between residues 203 F and 206 F 7 chains (1363 residues) following loop building 7 chains (1363 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12464 restraints for refining 12419 atoms. 799 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1748 (Rfree = 0.000) for 12419 atoms. Found 142 (142 requested) and removed 161 (142 requested) atoms. Cycle 32: After refmac, R = 0.1627 (Rfree = 0.000) for 12393 atoms. Found 142 (142 requested) and removed 144 (142 requested) atoms. Cycle 33: After refmac, R = 0.1576 (Rfree = 0.000) for 12387 atoms. Found 142 (142 requested) and removed 149 (142 requested) atoms. Cycle 34: After refmac, R = 0.1548 (Rfree = 0.000) for 12374 atoms. Found 142 (142 requested) and removed 154 (142 requested) atoms. Cycle 35: After refmac, R = 0.1538 (Rfree = 0.000) for 12358 atoms. Found 142 (142 requested) and removed 152 (142 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 2.02 NCS extension: 7 residues added (222 deleted due to clashes), 12368 seeds are put forward Round 1: 1323 peptides, 26 chains. Longest chain 139 peptides. Score 0.916 Round 2: 1323 peptides, 25 chains. Longest chain 140 peptides. Score 0.917 Round 3: 1315 peptides, 32 chains. Longest chain 140 peptides. Score 0.907 Round 4: 1327 peptides, 24 chains. Longest chain 140 peptides. Score 0.918 Round 5: 1314 peptides, 35 chains. Longest chain 140 peptides. Score 0.903 Taking the results from Round 4 Chains 26, Residues 1303, Estimated correctness of the model 98.9 % 24 chains (1297 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 108 A and 112 A Built loop between residues 132 A and 135 A Built loop between residues 156 A and 163 A Built loop between residues 195 A and 198 A Built loop between residues 106 C and 112 C Built loop between residues 156 C and 164 C Built loop between residues 185 C and 188 C Built loop between residues 203 C and 206 C Built loop between residues 95 B and 98 B Built loop between residues 156 B and 163 B Built loop between residues 204 B and 207 B Built loop between residues 156 E and 163 E Built loop between residues 155 D and 163 D Built loop between residues 204 D and 207 D Built loop between residues 156 F and 163 F Built loop between residues 204 F and 207 F 7 chains (1361 residues) following loop building 7 chains (1361 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12493 restraints for refining 12468 atoms. 843 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1824 (Rfree = 0.000) for 12468 atoms. Found 143 (143 requested) and removed 158 (143 requested) atoms. Cycle 37: After refmac, R = 0.1643 (Rfree = 0.000) for 12443 atoms. Found 143 (143 requested) and removed 144 (143 requested) atoms. Cycle 38: After refmac, R = 0.1580 (Rfree = 0.000) for 12436 atoms. Found 143 (143 requested) and removed 148 (143 requested) atoms. Cycle 39: After refmac, R = 0.1556 (Rfree = 0.000) for 12426 atoms. Found 142 (142 requested) and removed 155 (142 requested) atoms. Cycle 40: After refmac, R = 0.1552 (Rfree = 0.000) for 12404 atoms. Found 142 (142 requested) and removed 153 (142 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.17 2.03 NCS extension: 7 residues added (360 deleted due to clashes), 12410 seeds are put forward Round 1: 1317 peptides, 29 chains. Longest chain 139 peptides. Score 0.911 Round 2: 1313 peptides, 28 chains. Longest chain 140 peptides. Score 0.911 Round 3: 1313 peptides, 32 chains. Longest chain 87 peptides. Score 0.907 Round 4: 1312 peptides, 33 chains. Longest chain 84 peptides. Score 0.905 Round 5: 1311 peptides, 39 chains. Longest chain 140 peptides. Score 0.898 Taking the results from Round 2 Chains 30, Residues 1285, Estimated correctness of the model 98.7 % 27 chains (1279 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 164 A Built loop between residues 204 A and 207 A Built loop between residues 40 C and 43 C Built loop between residues 84 C and 87 C Built loop between residues 99 C and 102 C Built loop between residues 156 C and 164 C Built loop between residues 204 C and 207 C Built loop between residues 155 B and 163 B Built loop between residues 185 B and 188 B Built loop between residues 203 B and 206 B Built loop between residues 64 E and 71 E Built loop between residues 157 E and 164 E Built loop between residues 185 E and 188 E Built loop between residues 203 E and 206 E Built loop between residues 67 D and 70 D Built loop between residues 155 D and 162 D Built loop between residues 204 D and 207 D Built loop between residues 64 F and 73 F Built loop between residues 84 F and 87 F Built loop between residues 156 F and 165 F Built loop between residues 204 F and 207 F 6 chains (1360 residues) following loop building 6 chains (1360 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12492 restraints for refining 12416 atoms. 856 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1841 (Rfree = 0.000) for 12416 atoms. Found 142 (142 requested) and removed 157 (142 requested) atoms. Cycle 42: After refmac, R = 0.1644 (Rfree = 0.000) for 12395 atoms. Found 142 (142 requested) and removed 143 (142 requested) atoms. Cycle 43: After refmac, R = 0.1581 (Rfree = 0.000) for 12388 atoms. Found 142 (142 requested) and removed 149 (142 requested) atoms. Cycle 44: After refmac, R = 0.1558 (Rfree = 0.000) for 12378 atoms. Found 142 (142 requested) and removed 149 (142 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1541 (Rfree = 0.000) for 12368 atoms. Found 142 (142 requested) and removed 150 (142 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.16 2.02 NCS extension: 12 residues added (167 deleted due to clashes), 12384 seeds are put forward Round 1: 1325 peptides, 26 chains. Longest chain 139 peptides. Score 0.916 Round 2: 1317 peptides, 29 chains. Longest chain 140 peptides. Score 0.911 Round 3: 1323 peptides, 26 chains. Longest chain 140 peptides. Score 0.916 Round 4: 1313 peptides, 32 chains. Longest chain 128 peptides. Score 0.907 Round 5: 1310 peptides, 42 chains. Longest chain 121 peptides. Score 0.894 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 1297, Estimated correctness of the model 98.8 % 24 chains (1287 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 156 A and 163 A Built loop between residues 204 A and 207 A Built loop between residues 156 C and 164 C Built loop between residues 171 C and 174 C Built loop between residues 185 C and 196 C Built loop between residues 156 B and 163 B Built loop between residues 204 B and 207 B Built loop between residues 61 E and 70 E Built loop between residues 156 E and 162 E Built loop between residues 171 E and 174 E Built loop between residues 184 E and 187 E Built loop between residues 203 E and 206 E Built loop between residues 83 D and 86 D Built loop between residues 155 D and 163 D Built loop between residues 204 D and 207 D Built loop between residues 63 F and 66 F Built loop between residues 156 F and 164 F Built loop between residues 184 F and 187 F 6 chains (1363 residues) following loop building 6 chains (1363 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 78583 reflections ( 99.94 % complete ) and 11665 restraints for refining 11383 atoms. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2291 (Rfree = 0.000) for 11383 atoms. Found 110 (130 requested) and removed 0 (130 requested) atoms. Cycle 47: After refmac, R = 0.2098 (Rfree = 0.000) for 11383 atoms. Found 49 (132 requested) and removed 9 (132 requested) atoms. Cycle 48: After refmac, R = 0.2051 (Rfree = 0.000) for 11383 atoms. Found 29 (132 requested) and removed 10 (132 requested) atoms. Cycle 49: After refmac, R = 0.2018 (Rfree = 0.000) for 11383 atoms. TimeTaking 197.83