Mon 24 Dec 07:38:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2anu-2.3-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2anu-2.3-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2anu-2.3-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-parrot-noncs ############### 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 07:39:01 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/noncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 12240 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 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 13561 atoms. Observations/parameters ratio is 1.45 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2250 (Rfree = 0.000) for 13561 atoms. Found 256 (311 requested) and removed 165 (155 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.23 2.09 NCS extension: 0 residues added, 13652 seeds are put forward Round 1: 971 peptides, 126 chains. Longest chain 34 peptides. Score 0.581 Round 2: 1082 peptides, 92 chains. Longest chain 41 peptides. Score 0.734 Round 3: 1166 peptides, 68 chains. Longest chain 59 peptides. Score 0.816 Round 4: 1176 peptides, 68 chains. Longest chain 54 peptides. Score 0.820 Round 5: 1192 peptides, 54 chains. Longest chain 92 peptides. Score 0.848 Taking the results from Round 5 Chains 69, Residues 1138, Estimated correctness of the model 96.5 % 32 chains (951 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 85 A Built loop between residues 134 A and 139 A Built loop between residues 191 C and 197 C Built loop between residues 105 E and 115 E Built loop between residues 206 E and 213 E Built loop between residues 40 F and 44 F Built loop between residues 190 F and 196 F 58 chains (1164 residues) following loop building 25 chains (984 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 15972 restraints for refining 12622 atoms. 7020 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2551 (Rfree = 0.000) for 12622 atoms. Found 290 (290 requested) and removed 199 (145 requested) atoms. Cycle 2: After refmac, R = 0.2303 (Rfree = 0.000) for 12616 atoms. Found 227 (286 requested) and removed 156 (146 requested) atoms. Cycle 3: After refmac, R = 0.2179 (Rfree = 0.000) for 12628 atoms. Found 191 (279 requested) and removed 150 (145 requested) atoms. Cycle 4: After refmac, R = 0.2095 (Rfree = 0.000) for 12613 atoms. Found 166 (274 requested) and removed 158 (145 requested) atoms. Cycle 5: After refmac, R = 0.2031 (Rfree = 0.000) for 12582 atoms. Found 190 (267 requested) and removed 153 (145 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.18 2.04 NCS extension: 201 residues added (551 deleted due to clashes), 12842 seeds are put forward Round 1: 1250 peptides, 40 chains. Longest chain 81 peptides. Score 0.884 Round 2: 1259 peptides, 37 chains. Longest chain 99 peptides. Score 0.890 Round 3: 1279 peptides, 32 chains. Longest chain 82 peptides. Score 0.900 Round 4: 1267 peptides, 42 chains. Longest chain 128 peptides. Score 0.885 Round 5: 1281 peptides, 41 chains. Longest chain 91 peptides. Score 0.889 Taking the results from Round 3 Chains 37, Residues 1247, Estimated correctness of the model 98.4 % 25 chains (1172 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 186 B and 191 B Built loop between residues 65 E and 76 E Built loop between residues 203 E and 206 E Built loop between residues 63 D and 67 D Built loop between residues 144 D and 147 D Built loop between residues 156 D and 166 D Built loop between residues 61 F and 65 F Built loop between residues 177 F and 180 F 23 chains (1287 residues) following loop building 14 chains (1218 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 13467 restraints for refining 12484 atoms. 2877 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2162 (Rfree = 0.000) for 12484 atoms. Found 258 (258 requested) and removed 180 (143 requested) atoms. Cycle 7: After refmac, R = 0.1961 (Rfree = 0.000) for 12526 atoms. Found 253 (253 requested) and removed 154 (144 requested) atoms. Cycle 8: After refmac, R = 0.1849 (Rfree = 0.000) for 12593 atoms. Found 246 (249 requested) and removed 157 (145 requested) atoms. Cycle 9: After refmac, R = 0.1788 (Rfree = 0.000) for 12658 atoms. Found 225 (244 requested) and removed 160 (145 requested) atoms. Cycle 10: After refmac, R = 0.1730 (Rfree = 0.000) for 12700 atoms. Found 239 (239 requested) and removed 162 (146 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.16 2.02 NCS extension: 127 residues added (1308 deleted due to clashes), 12917 seeds are put forward Round 1: 1296 peptides, 31 chains. Longest chain 140 peptides. Score 0.905 Round 2: 1299 peptides, 27 chains. Longest chain 140 peptides. Score 0.910 Round 3: 1293 peptides, 33 chains. Longest chain 140 peptides. Score 0.902 Round 4: 1293 peptides, 34 chains. Longest chain 140 peptides. Score 0.900 Round 5: 1297 peptides, 35 chains. Longest chain 87 peptides. Score 0.900 Taking the results from Round 2 Chains 27, Residues 1272, Estimated correctness of the model 98.6 % 25 chains (1259 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 165 A Built loop between residues 204 A and 207 A Built loop between residues 66 C and 73 C Built loop between residues 84 C and 87 C Built loop between residues 155 C and 166 C Built loop between residues 203 C and 206 C Built loop between residues 42 B and 45 B Built loop between residues 64 B and 70 B Built loop between residues 83 B and 86 B Built loop between residues 155 B and 165 B Built loop between residues 204 B and 207 B Built loop between residues 155 E and 164 E Built loop between residues 204 E and 207 E Built loop between residues 156 D and 165 D Built loop between residues 204 D and 207 D Built loop between residues 67 F and 72 F Built loop between residues 154 F and 164 F Built loop between residues 194 F and 197 F Built loop between residues 204 F and 212 F 7 chains (1361 residues) following loop building 6 chains (1351 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12788 restraints for refining 12696 atoms. 1195 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1985 (Rfree = 0.000) for 12696 atoms. Found 234 (234 requested) and removed 177 (146 requested) atoms. Cycle 12: After refmac, R = 0.1799 (Rfree = 0.000) for 12722 atoms. Found 229 (229 requested) and removed 156 (146 requested) atoms. Cycle 13: After refmac, R = 0.1714 (Rfree = 0.000) for 12778 atoms. Found 223 (223 requested) and removed 160 (147 requested) atoms. Cycle 14: After refmac, R = 0.1665 (Rfree = 0.000) for 12827 atoms. Found 218 (218 requested) and removed 170 (147 requested) atoms. Cycle 15: After refmac, R = 0.1635 (Rfree = 0.000) for 12861 atoms. Found 213 (213 requested) and removed 175 (148 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.16 2.02 NCS extension: 12 residues added (167 deleted due to clashes), 12927 seeds are put forward Round 1: 1322 peptides, 23 chains. Longest chain 141 peptides. Score 0.919 Round 2: 1309 peptides, 31 chains. Longest chain 140 peptides. Score 0.907 Round 3: 1322 peptides, 24 chains. Longest chain 140 peptides. Score 0.918 Round 4: 1308 peptides, 39 chains. Longest chain 140 peptides. Score 0.897 Round 5: 1307 peptides, 32 chains. Longest chain 121 peptides. Score 0.906 Taking the results from Round 1 Chains 28, Residues 1299, Estimated correctness of the model 98.9 % 24 chains (1286 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 165 A Built loop between residues 203 A and 206 A Built loop between residues 156 C and 163 C Built loop between residues 185 C and 188 C Built loop between residues 203 C and 206 C Built loop between residues 67 B and 73 B Built loop between residues 156 B and 165 B Built loop between residues 204 B and 207 B 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 156 D and 164 D Built loop between residues 204 D and 207 D Built loop between residues 156 F and 165 F Built loop between residues 185 F and 188 F Built loop between residues 203 F and 206 F 8 chains (1364 residues) following loop building 7 chains (1354 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12450 restraints for refining 12474 atoms. 823 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1819 (Rfree = 0.000) for 12474 atoms. Found 200 (200 requested) and removed 162 (143 requested) atoms. Cycle 17: After refmac, R = 0.1686 (Rfree = 0.000) for 12494 atoms. Found 195 (195 requested) and removed 145 (143 requested) atoms. Cycle 18: After refmac, R = 0.1614 (Rfree = 0.000) for 12535 atoms. Found 190 (190 requested) and removed 153 (144 requested) atoms. Cycle 19: After refmac, R = 0.1569 (Rfree = 0.000) for 12561 atoms. Found 185 (185 requested) and removed 158 (144 requested) atoms. Cycle 20: After refmac, R = 0.1537 (Rfree = 0.000) for 12579 atoms. Found 179 (179 requested) and removed 164 (144 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.16 2.02 NCS extension: 23 residues added (378 deleted due to clashes), 12640 seeds are put forward Round 1: 1321 peptides, 27 chains. Longest chain 139 peptides. Score 0.914 Round 2: 1314 peptides, 27 chains. Longest chain 140 peptides. Score 0.913 Round 3: 1309 peptides, 27 chains. Longest chain 140 peptides. Score 0.912 Round 4: 1299 peptides, 36 chains. Longest chain 87 peptides. Score 0.899 Round 5: 1316 peptides, 29 chains. Longest chain 141 peptides. Score 0.911 Taking the results from Round 1 Chains 32, Residues 1294, Estimated correctness of the model 98.8 % 27 chains (1289 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 63 C and 66 C Built loop between residues 157 C and 162 C Built loop between residues 204 C and 207 C Built loop between residues 155 B and 165 B Built loop between residues 185 B and 188 B Built loop between residues 203 B and 206 B Built loop between residues 83 E and 86 E Built loop between residues 156 E and 164 E Built loop between residues 203 E and 206 E Built loop between residues 155 D and 164 D Built loop between residues 203 D and 206 D Built loop between residues 67 F and 72 F Built loop between residues 83 F and 86 F Built loop between residues 156 F and 164 F Built loop between residues 186 F and 188 F Built loop between residues 203 F and 206 F 12 chains (1362 residues) following loop building 8 chains (1358 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12451 restraints for refining 12431 atoms. 818 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1770 (Rfree = 0.000) for 12431 atoms. Found 171 (171 requested) and removed 152 (142 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1639 (Rfree = 0.000) for 12434 atoms. Found 166 (166 requested) and removed 145 (143 requested) atoms. Cycle 23: After refmac, R = 0.1586 (Rfree = 0.000) for 12441 atoms. Found 160 (160 requested) and removed 147 (143 requested) atoms. Cycle 24: After refmac, R = 0.1550 (Rfree = 0.000) for 12446 atoms. Found 154 (154 requested) and removed 154 (143 requested) atoms. Cycle 25: After refmac, R = 0.1528 (Rfree = 0.000) for 12438 atoms. Found 149 (149 requested) and removed 146 (143 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.16 2.02 NCS extension: 11 residues added (392 deleted due to clashes), 12465 seeds are put forward Round 1: 1320 peptides, 25 chains. Longest chain 140 peptides. Score 0.916 Round 2: 1307 peptides, 26 chains. Longest chain 140 peptides. Score 0.913 Round 3: 1315 peptides, 24 chains. Longest chain 140 peptides. Score 0.916 Round 4: 1316 peptides, 27 chains. Longest chain 140 peptides. Score 0.913 Round 5: 1315 peptides, 31 chains. Longest chain 121 peptides. Score 0.908 Taking the results from Round 3 Chains 24, Residues 1291, Estimated correctness of the model 98.8 % 23 chains (1208 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 164 A Built loop between residues 185 A and 188 A Built loop between residues 203 A and 206 A Built loop between residues 156 B and 164 B Built loop between residues 203 B and 206 B Built loop between residues 68 E and 72 E Built loop between residues 156 E and 164 E Built loop between residues 184 E and 187 E Built loop between residues 67 D and 70 D Built loop between residues 156 D and 163 D Built loop between residues 204 D and 207 D Built loop between residues 74 F and 77 F Built loop between residues 99 F and 102 F Built loop between residues 155 F and 164 F Built loop between residues 204 F and 207 F 9 chains (1347 residues) following loop building 8 chains (1264 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 13152 restraints for refining 12316 atoms. 2043 conditional restraints added. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1775 (Rfree = 0.000) for 12316 atoms. Found 141 (141 requested) and removed 150 (141 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1656 (Rfree = 0.000) for 12293 atoms. Found 141 (141 requested) and removed 141 (141 requested) atoms. Cycle 28: After refmac, R = 0.1602 (Rfree = 0.000) for 12285 atoms. Found 141 (141 requested) and removed 144 (141 requested) atoms. Cycle 29: After refmac, R = 0.1571 (Rfree = 0.000) for 12275 atoms. Found 141 (141 requested) and removed 148 (141 requested) atoms. Cycle 30: After refmac, R = 0.1551 (Rfree = 0.000) for 12258 atoms. Found 141 (141 requested) and removed 152 (141 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.16 2.02 NCS extension: 39 residues added (735 deleted due to clashes), 12300 seeds are put forward Round 1: 1318 peptides, 28 chains. Longest chain 139 peptides. Score 0.912 Round 2: 1320 peptides, 27 chains. Longest chain 170 peptides. Score 0.914 Round 3: 1322 peptides, 24 chains. Longest chain 140 peptides. Score 0.918 Round 4: 1324 peptides, 26 chains. Longest chain 162 peptides. Score 0.916 Round 5: 1320 peptides, 33 chains. Longest chain 140 peptides. Score 0.907 Taking the results from Round 3 Chains 24, Residues 1298, Estimated correctness of the model 98.9 % 22 chains (1287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 63 A Built loop between residues 144 A and 147 A Built loop between residues 156 A and 163 A Built loop between residues 108 C and 111 C Built loop between residues 155 C and 164 C Built loop between residues 204 C and 207 C Built loop between residues 156 B and 164 B Built loop between residues 171 B and 174 B Built loop between residues 156 E and 163 E Built loop between residues 204 E and 207 E Built loop between residues 156 D and 162 D Built loop between residues 204 D and 207 D Built loop between residues 155 F and 163 F Built loop between residues 178 F and 187 F Built loop between residues 203 F and 206 F 8 chains (1357 residues) following loop building 7 chains (1350 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12456 restraints for refining 12401 atoms. 873 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1791 (Rfree = 0.000) for 12401 atoms. Found 142 (142 requested) and removed 153 (142 requested) atoms. Cycle 32: After refmac, R = 0.1639 (Rfree = 0.000) for 12376 atoms. Found 142 (142 requested) and removed 144 (142 requested) atoms. Cycle 33: After refmac, R = 0.1591 (Rfree = 0.000) for 12368 atoms. Found 142 (142 requested) and removed 147 (142 requested) atoms. Cycle 34: After refmac, R = 0.1552 (Rfree = 0.000) for 12358 atoms. Found 142 (142 requested) and removed 150 (142 requested) atoms. Cycle 35: After refmac, R = 0.1542 (Rfree = 0.000) for 12343 atoms. Found 142 (142 requested) and removed 153 (142 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 2.02 NCS extension: 11 residues added (310 deleted due to clashes), 12359 seeds are put forward Round 1: 1313 peptides, 28 chains. Longest chain 139 peptides. Score 0.911 Round 2: 1319 peptides, 24 chains. Longest chain 139 peptides. Score 0.917 Round 3: 1314 peptides, 28 chains. Longest chain 139 peptides. Score 0.912 Round 4: 1324 peptides, 28 chains. Longest chain 140 peptides. Score 0.913 Round 5: 1305 peptides, 34 chains. Longest chain 82 peptides. Score 0.903 Taking the results from Round 2 Chains 27, Residues 1295, Estimated correctness of the model 98.8 % 24 chains (1292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 164 A Built loop between residues 185 A and 188 A Built loop between residues 203 A and 206 A Built loop between residues 61 C and 64 C Built loop between residues 83 C and 86 C Built loop between residues 156 C and 163 C Built loop between residues 204 C and 207 C Built loop between residues 156 B and 163 B Built loop between residues 204 B and 207 B Built loop between residues 155 E and 163 E Built loop between residues 204 E and 207 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 41 F and 44 F Built loop between residues 67 F and 71 F Built loop between residues 83 F and 86 F Built loop between residues 155 F and 164 F 6 chains (1359 residues) following loop building 6 chains (1359 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12421 restraints for refining 12375 atoms. 794 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1761 (Rfree = 0.000) for 12375 atoms. Found 142 (142 requested) and removed 161 (142 requested) atoms. Cycle 37: After refmac, R = 0.1632 (Rfree = 0.000) for 12345 atoms. Found 142 (142 requested) and removed 143 (142 requested) atoms. Cycle 38: After refmac, R = 0.1572 (Rfree = 0.000) for 12340 atoms. Found 141 (141 requested) and removed 149 (141 requested) atoms. Cycle 39: After refmac, R = 0.1549 (Rfree = 0.000) for 12327 atoms. Found 141 (141 requested) and removed 150 (141 requested) atoms. Cycle 40: After refmac, R = 0.1539 (Rfree = 0.000) for 12313 atoms. Found 141 (141 requested) and removed 149 (141 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.17 2.03 NCS extension: 8 residues added (167 deleted due to clashes), 12323 seeds are put forward Round 1: 1312 peptides, 28 chains. Longest chain 140 peptides. Score 0.911 Round 2: 1315 peptides, 27 chains. Longest chain 95 peptides. Score 0.913 Round 3: 1316 peptides, 27 chains. Longest chain 140 peptides. Score 0.913 Round 4: 1308 peptides, 31 chains. Longest chain 140 peptides. Score 0.907 Round 5: 1306 peptides, 35 chains. Longest chain 94 peptides. Score 0.902 Taking the results from Round 3 Chains 28, Residues 1289, Estimated correctness of the model 98.7 % 24 chains (1194 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 156 A and 164 A Built loop between residues 171 A and 174 A Built loop between residues 43 C and 46 C Built loop between residues 156 C and 164 C Built loop between residues 67 B and 70 B Built loop between residues 156 E and 164 E Built loop between residues 171 E and 174 E Built loop between residues 193 E and 196 E Built loop between residues 156 D and 164 D Built loop between residues 205 D and 208 D Built loop between residues 108 F and 111 F Built loop between residues 155 F and 164 F 15 chains (1341 residues) following loop building 11 chains (1246 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 13162 restraints for refining 12219 atoms. 2159 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1763 (Rfree = 0.000) for 12219 atoms. Found 140 (140 requested) and removed 151 (140 requested) atoms. Cycle 42: After refmac, R = 0.1617 (Rfree = 0.000) for 12194 atoms. Found 140 (140 requested) and removed 143 (140 requested) atoms. Cycle 43: After refmac, R = 0.1567 (Rfree = 0.000) for 12186 atoms. Found 140 (140 requested) and removed 143 (140 requested) atoms. Cycle 44: After refmac, R = 0.1541 (Rfree = 0.000) for 12178 atoms. Found 140 (140 requested) and removed 149 (140 requested) atoms. Cycle 45: After refmac, R = 0.1534 (Rfree = 0.000) for 12161 atoms. Found 139 (139 requested) and removed 144 (139 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.16 2.02 NCS extension: 30 residues added (603 deleted due to clashes), 12205 seeds are put forward Round 1: 1315 peptides, 27 chains. Longest chain 139 peptides. Score 0.913 Round 2: 1314 peptides, 25 chains. Longest chain 139 peptides. Score 0.915 Round 3: 1308 peptides, 32 chains. Longest chain 140 peptides. Score 0.906 Round 4: 1311 peptides, 29 chains. Longest chain 140 peptides. Score 0.910 Round 5: 1304 peptides, 37 chains. Longest chain 121 peptides. Score 0.899 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 1289, Estimated correctness of the model 98.8 % 25 chains (1285 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 155 A and 163 A Built loop between residues 204 A and 207 A Built loop between residues 68 C and 72 C Built loop between residues 157 C and 164 C Built loop between residues 171 C and 174 C Built loop between residues 203 C and 206 C Built loop between residues 74 B and 77 B Built loop between residues 155 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 164 E Built loop between residues 204 E and 207 E Built loop between residues 83 D and 86 D Built loop between residues 155 D and 164 D Built loop between residues 184 D and 187 D Built loop between residues 69 F and 73 F Built loop between residues 82 F and 86 F Built loop between residues 156 F and 165 F Built loop between residues 204 F and 207 F 6 chains (1358 residues) following loop building 6 chains (1358 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 78583 reflections ( 99.94 % complete ) and 11618 restraints for refining 11336 atoms. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2285 (Rfree = 0.000) for 11336 atoms. Found 122 (130 requested) and removed 0 (130 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 11336 atoms. Found 62 (131 requested) and removed 15 (131 requested) atoms. Cycle 48: After refmac, R = 0.2043 (Rfree = 0.000) for 11336 atoms. Found 38 (132 requested) and removed 7 (132 requested) atoms. Cycle 49: After refmac, R = 0.1994 (Rfree = 0.000) for 11336 atoms. TimeTaking 220.5