null Tue 25 Dec 19:27:55 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 2anu-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2anu-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2anu-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-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/2anu-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-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 ============================================================ Tue 25 Dec 19:28:04 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/2anu-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-2.3-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 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-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-2.3-parrot-hancs.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 13496 atoms. Observations/parameters ratio is 1.46 ------------------------------------------------------ Starting model: R = 0.2804 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1982 (Rfree = 0.000) for 13496 atoms. Found 310 (310 requested) and removed 162 (155 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.20 2.06 NCS extension: 0 residues added, 13644 seeds are put forward Round 1: 1021 peptides, 119 chains. Longest chain 35 peptides. Score 0.633 Round 2: 1183 peptides, 78 chains. Longest chain 46 peptides. Score 0.804 Round 3: 1238 peptides, 54 chains. Longest chain 79 peptides. Score 0.861 Round 4: 1265 peptides, 45 chains. Longest chain 83 peptides. Score 0.880 Round 5: 1283 peptides, 34 chains. Longest chain 128 peptides. Score 0.899 Taking the results from Round 5 Chains 36, Residues 1249, Estimated correctness of the model 98.3 % 28 chains (1193 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 74 A Built loop between residues 136 A and 139 A Built loop between residues 185 A and 192 A Built loop between residues 203 A and 206 A Built loop between residues 154 C and 164 C Built loop between residues 81 B and 85 B Built loop between residues 133 B and 136 B Built loop between residues 204 B and 207 B Built loop between residues 227 B and 230 B Built loop between residues 154 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 179 D and 182 D Built loop between residues 68 F and 74 F Built loop between residues 155 F and 166 F 20 chains (1312 residues) following loop building 13 chains (1257 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 13661 restraints for refining 12734 atoms. 2694 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2197 (Rfree = 0.000) for 12734 atoms. Found 293 (293 requested) and removed 199 (146 requested) atoms. Cycle 2: After refmac, R = 0.1973 (Rfree = 0.000) for 12738 atoms. Found 260 (289 requested) and removed 174 (147 requested) atoms. Cycle 3: After refmac, R = 0.1882 (Rfree = 0.000) for 12775 atoms. Found 259 (282 requested) and removed 165 (147 requested) atoms. Cycle 4: After refmac, R = 0.1799 (Rfree = 0.000) for 12841 atoms. Found 232 (278 requested) and removed 172 (148 requested) atoms. Cycle 5: After refmac, R = 0.1742 (Rfree = 0.000) for 12871 atoms. Found 242 (272 requested) and removed 178 (148 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.17 2.03 NCS extension: 53 residues added (923 deleted due to clashes), 13003 seeds are put forward Round 1: 1306 peptides, 31 chains. Longest chain 84 peptides. Score 0.907 Round 2: 1313 peptides, 23 chains. Longest chain 140 peptides. Score 0.917 Round 3: 1313 peptides, 27 chains. Longest chain 140 peptides. Score 0.913 Round 4: 1313 peptides, 26 chains. Longest chain 140 peptides. Score 0.914 Round 5: 1307 peptides, 39 chains. Longest chain 80 peptides. Score 0.897 Taking the results from Round 2 Chains 23, Residues 1290, Estimated correctness of the model 98.8 % 22 chains (1245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 73 A Built loop between residues 154 A and 164 A Built loop between residues 171 A and 174 A Built loop between residues 203 A and 206 A Built loop between residues 63 C and 66 C Built loop between residues 155 C and 164 C Built loop between residues 204 C and 207 C Built loop between residues 83 B and 86 B Built loop between residues 156 B and 163 B Built loop between residues 183 E and 186 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 162 F Built loop between residues 204 F and 207 F 9 chains (1345 residues) following loop building 8 chains (1300 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12988 restraints for refining 12514 atoms. 1669 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1913 (Rfree = 0.000) for 12514 atoms. Found 258 (258 requested) and removed 155 (143 requested) atoms. Cycle 7: After refmac, R = 0.1768 (Rfree = 0.000) for 12590 atoms. Found 255 (255 requested) and removed 156 (145 requested) atoms. Cycle 8: After refmac, R = 0.1685 (Rfree = 0.000) for 12670 atoms. Found 250 (250 requested) and removed 158 (145 requested) atoms. Cycle 9: After refmac, R = 0.1640 (Rfree = 0.000) for 12753 atoms. Found 246 (246 requested) and removed 172 (146 requested) atoms. Cycle 10: After refmac, R = 0.1608 (Rfree = 0.000) for 12812 atoms. Found 242 (242 requested) and removed 175 (147 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.17 2.03 NCS extension: 11 residues added (428 deleted due to clashes), 12903 seeds are put forward Round 1: 1307 peptides, 28 chains. Longest chain 140 peptides. Score 0.910 Round 2: 1317 peptides, 22 chains. Longest chain 140 peptides. Score 0.919 Round 3: 1309 peptides, 31 chains. Longest chain 140 peptides. Score 0.907 Round 4: 1311 peptides, 32 chains. Longest chain 106 peptides. Score 0.906 Round 5: 1301 peptides, 35 chains. Longest chain 140 peptides. Score 0.901 Taking the results from Round 2 Chains 22, Residues 1295, Estimated correctness of the model 98.9 % 21 chains (1275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 144 A and 147 A Built loop between residues 156 A and 164 A Built loop between residues 204 A and 207 A Built loop between residues 84 C and 87 C Built loop between residues 155 C and 164 C Built loop between residues 204 C and 207 C Built loop between residues 66 B and 72 B Built loop between residues 155 B and 164 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 163 D Built loop between residues 68 F and 73 F Built loop between residues 155 F and 165 F Built loop between residues 204 F and 207 F 8 chains (1360 residues) following loop building 7 chains (1340 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12759 restraints for refining 12515 atoms. 1196 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1861 (Rfree = 0.000) for 12515 atoms. Found 230 (230 requested) and removed 161 (143 requested) atoms. Cycle 12: After refmac, R = 0.1700 (Rfree = 0.000) for 12569 atoms. Found 225 (225 requested) and removed 149 (144 requested) atoms. Cycle 13: After refmac, R = 0.1626 (Rfree = 0.000) for 12628 atoms. Found 220 (220 requested) and removed 152 (145 requested) atoms. Cycle 14: After refmac, R = 0.1595 (Rfree = 0.000) for 12692 atoms. Found 216 (216 requested) and removed 162 (146 requested) atoms. Cycle 15: After refmac, R = 0.1560 (Rfree = 0.000) for 12739 atoms. Found 211 (211 requested) and removed 159 (146 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.16 2.02 NCS extension: 15 residues added (262 deleted due to clashes), 12815 seeds are put forward Round 1: 1326 peptides, 26 chains. Longest chain 140 peptides. Score 0.916 Round 2: 1308 peptides, 27 chains. Longest chain 140 peptides. Score 0.912 Round 3: 1315 peptides, 34 chains. Longest chain 94 peptides. Score 0.905 Round 4: 1330 peptides, 25 chains. Longest chain 140 peptides. Score 0.918 Round 5: 1316 peptides, 32 chains. Longest chain 139 peptides. Score 0.907 Taking the results from Round 4 Chains 26, Residues 1305, Estimated correctness of the model 98.9 % 23 chains (1236 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 161 A Built loop between residues 204 A and 207 A Built loop between residues 102 B and 105 B Built loop between residues 156 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 156 E and 162 E Built loop between residues 204 E and 207 E Built loop between residues 65 D and 69 D Built loop between residues 156 D and 163 D Built loop between residues 186 D and 188 D Built loop between residues 203 D and 206 D Built loop between residues 60 F and 63 F Built loop between residues 156 F and 163 F Built loop between residues 204 F and 207 F 10 chains (1352 residues) following loop building 8 chains (1284 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 13183 restraints for refining 12448 atoms. 1932 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1808 (Rfree = 0.000) for 12448 atoms. Found 200 (200 requested) and removed 161 (143 requested) atoms. Cycle 17: After refmac, R = 0.1665 (Rfree = 0.000) for 12473 atoms. Found 195 (195 requested) and removed 147 (143 requested) atoms. Cycle 18: After refmac, R = 0.1600 (Rfree = 0.000) for 12516 atoms. Found 190 (190 requested) and removed 157 (144 requested) atoms. Cycle 19: After refmac, R = 0.1572 (Rfree = 0.000) for 12543 atoms. Found 184 (184 requested) and removed 156 (144 requested) atoms. Cycle 20: After refmac, R = 0.1552 (Rfree = 0.000) for 12561 atoms. Found 179 (179 requested) and removed 158 (144 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.16 2.02 NCS extension: 2 residues added (169 deleted due to clashes), 12599 seeds are put forward Round 1: 1318 peptides, 30 chains. Longest chain 93 peptides. Score 0.910 Round 2: 1325 peptides, 26 chains. Longest chain 140 peptides. Score 0.916 Round 3: 1325 peptides, 32 chains. Longest chain 140 peptides. Score 0.909 Round 4: 1320 peptides, 32 chains. Longest chain 140 peptides. Score 0.908 Round 5: 1315 peptides, 37 chains. Longest chain 127 peptides. Score 0.901 Taking the results from Round 2 Chains 27, Residues 1299, Estimated correctness of the model 98.8 % 25 chains (1274 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 71 A Built loop between residues 83 A and 86 A Built loop between residues 156 A and 162 A Built loop between residues 204 A and 207 A 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 83 B and 86 B Built loop between residues 156 B and 164 B Built loop between residues 204 B and 207 B Built loop between residues 156 E and 164 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 100 F and 103 F Built loop between residues 156 F and 164 F Built loop between residues 185 F and 188 F Built loop between residues 203 F and 206 F 7 chains (1363 residues) following loop building 6 chains (1339 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12706 restraints for refining 12470 atoms. 1143 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1779 (Rfree = 0.000) for 12470 atoms. Found 172 (172 requested) and removed 158 (143 requested) atoms. Cycle 22: After refmac, R = 0.1645 (Rfree = 0.000) for 12474 atoms. Found 166 (166 requested) and removed 143 (143 requested) atoms. Cycle 23: After refmac, R = 0.1591 (Rfree = 0.000) for 12489 atoms. Found 161 (161 requested) and removed 144 (143 requested) atoms. Cycle 24: After refmac, R = 0.1571 (Rfree = 0.000) for 12499 atoms. Found 155 (155 requested) and removed 153 (143 requested) atoms. Cycle 25: After refmac, R = 0.1557 (Rfree = 0.000) for 12495 atoms. Found 149 (149 requested) and removed 156 (143 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.16 2.02 NCS extension: 22 residues added (630 deleted due to clashes), 12526 seeds are put forward Round 1: 1319 peptides, 30 chains. Longest chain 140 peptides. Score 0.910 Round 2: 1326 peptides, 25 chains. Longest chain 140 peptides. Score 0.917 Round 3: 1330 peptides, 31 chains. Longest chain 170 peptides. Score 0.911 Round 4: 1326 peptides, 30 chains. Longest chain 140 peptides. Score 0.911 Round 5: 1323 peptides, 34 chains. Longest chain 113 peptides. Score 0.906 Taking the results from Round 2 Chains 25, Residues 1301, Estimated correctness of the model 98.8 % 24 chains (1294 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 164 A Built loop between residues 192 A and 195 A Built loop between residues 203 A and 206 A Built loop between residues 156 C and 163 C Built loop between residues 204 C and 207 C Built loop between residues 66 B and 69 B Built loop between residues 157 B and 164 B Built loop between residues 204 B and 207 B Built loop between residues 64 E and 67 E Built loop between residues 83 E and 86 E Built loop between residues 157 E and 161 E Built loop between residues 204 E and 207 E Built loop between residues 156 D and 162 D Built loop between residues 41 F and 44 F Built loop between residues 99 F and 102 F Built loop between residues 156 F and 164 F Built loop between residues 204 F and 207 F 8 chains (1357 residues) following loop building 7 chains (1350 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12594 restraints for refining 12390 atoms. 1014 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1777 (Rfree = 0.000) for 12390 atoms. Found 142 (142 requested) and removed 157 (142 requested) atoms. Cycle 27: After refmac, R = 0.1649 (Rfree = 0.000) for 12365 atoms. Found 142 (142 requested) and removed 143 (142 requested) atoms. Cycle 28: After refmac, R = 0.1592 (Rfree = 0.000) for 12354 atoms. Found 142 (142 requested) and removed 148 (142 requested) atoms. Cycle 29: After refmac, R = 0.1590 (Rfree = 0.000) for 12341 atoms. Found 142 (142 requested) and removed 147 (142 requested) atoms. Cycle 30: After refmac, R = 0.1561 (Rfree = 0.000) for 12329 atoms. Found 141 (141 requested) and removed 148 (141 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.17 2.03 NCS extension: 21 residues added (491 deleted due to clashes), 12359 seeds are put forward Round 1: 1312 peptides, 31 chains. Longest chain 139 peptides. Score 0.908 Round 2: 1314 peptides, 25 chains. Longest chain 140 peptides. Score 0.915 Round 3: 1311 peptides, 34 chains. Longest chain 139 peptides. Score 0.904 Round 4: 1307 peptides, 35 chains. Longest chain 127 peptides. Score 0.902 Round 5: 1306 peptides, 34 chains. Longest chain 139 peptides. Score 0.903 Taking the results from Round 2 Chains 25, Residues 1289, Estimated correctness of the model 98.8 % 24 chains (1277 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 156 C and 164 C Built loop between residues 204 C and 207 C Built loop between residues 84 B and 87 B Built loop between residues 99 B and 102 B Built loop between residues 156 B and 164 B Built loop between residues 204 B and 207 B Built loop between residues 156 E and 164 E Built loop between residues 191 E and 194 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 84 F and 87 F Built loop between residues 155 F and 165 F Built loop between residues 204 F and 207 F 8 chains (1355 residues) following loop building 7 chains (1343 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12555 restraints for refining 12355 atoms. 1010 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1896 (Rfree = 0.000) for 12355 atoms. Found 142 (142 requested) and removed 157 (142 requested) atoms. Cycle 32: After refmac, R = 0.1717 (Rfree = 0.000) for 12328 atoms. Found 141 (141 requested) and removed 141 (141 requested) atoms. Cycle 33: After refmac, R = 0.1667 (Rfree = 0.000) for 12318 atoms. Found 141 (141 requested) and removed 146 (141 requested) atoms. Cycle 34: After refmac, R = 0.1633 (Rfree = 0.000) for 12308 atoms. Found 141 (141 requested) and removed 144 (141 requested) atoms. Cycle 35: After refmac, R = 0.1587 (Rfree = 0.000) for 12298 atoms. Found 141 (141 requested) and removed 148 (141 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 2.02 NCS extension: 14 residues added (544 deleted due to clashes), 12313 seeds are put forward Round 1: 1322 peptides, 31 chains. Longest chain 139 peptides. Score 0.909 Round 2: 1327 peptides, 23 chains. Longest chain 140 peptides. Score 0.919 Round 3: 1323 peptides, 32 chains. Longest chain 140 peptides. Score 0.909 Round 4: 1328 peptides, 27 chains. Longest chain 127 peptides. Score 0.915 Round 5: 1322 peptides, 30 chains. Longest chain 140 peptides. Score 0.911 Taking the results from Round 2 Chains 23, Residues 1304, Estimated correctness of the model 98.9 % 23 chains (1304 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 164 A Built loop between residues 155 C and 161 C Built loop between residues 177 C and 180 C Built loop between residues 203 C and 206 C Built loop between residues 64 B and 67 B Built loop between residues 81 B and 85 B Built loop between residues 157 B and 164 B Built loop between residues 204 B and 207 B Built loop between residues 63 E and 66 E Built loop between residues 157 E and 161 E Built loop between residues 204 E and 207 E Built loop between residues 156 D and 164 D Built loop between residues 204 D and 207 D Built loop between residues 84 F and 87 F Built loop between residues 99 F and 102 F Built loop between residues 157 F and 164 F Built loop between residues 204 F and 207 F 6 chains (1361 residues) following loop building 6 chains (1361 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12435 restraints for refining 12390 atoms. 789 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1900 (Rfree = 0.000) for 12390 atoms. Found 142 (142 requested) and removed 153 (142 requested) atoms. Cycle 37: After refmac, R = 0.1740 (Rfree = 0.000) for 12375 atoms. Found 142 (142 requested) and removed 142 (142 requested) atoms. Cycle 38: After refmac, R = 0.1676 (Rfree = 0.000) for 12370 atoms. Found 142 (142 requested) and removed 145 (142 requested) atoms. Cycle 39: After refmac, R = 0.1639 (Rfree = 0.000) for 12363 atoms. Found 142 (142 requested) and removed 147 (142 requested) atoms. Cycle 40: After refmac, R = 0.1618 (Rfree = 0.000) for 12356 atoms. Found 142 (142 requested) and removed 147 (142 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.17 2.03 NCS extension: 4 residues added (82 deleted due to clashes), 12362 seeds are put forward Round 1: 1320 peptides, 28 chains. Longest chain 140 peptides. Score 0.913 Round 2: 1320 peptides, 27 chains. Longest chain 140 peptides. Score 0.914 Round 3: 1321 peptides, 24 chains. Longest chain 141 peptides. Score 0.917 Round 4: 1322 peptides, 25 chains. Longest chain 140 peptides. Score 0.916 Round 5: 1301 peptides, 41 chains. Longest chain 140 peptides. Score 0.893 Taking the results from Round 3 Chains 24, Residues 1297, Estimated correctness of the model 98.8 % 23 chains (1289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 163 A Built loop between residues 184 A and 187 A Built loop between residues 61 C and 64 C Built loop between residues 83 C and 86 C Built loop between residues 184 C and 187 C Built loop between residues 204 C and 207 C Built loop between residues 63 B and 66 B Built loop between residues 156 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 157 E and 164 E Built loop between residues 204 E and 207 E 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 162 F Built loop between residues 204 F and 207 F 8 chains (1351 residues) following loop building 7 chains (1343 residues) in sequence following loop building ------------------------------------------------------ 78583 reflections ( 99.94 % complete ) and 12613 restraints for refining 12369 atoms. 1108 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1761 (Rfree = 0.000) for 12369 atoms. Found 142 (142 requested) and removed 161 (142 requested) atoms. Cycle 42: After refmac, R = 0.1637 (Rfree = 0.000) for 12346 atoms. Found 142 (142 requested) and removed 148 (142 requested) atoms. Cycle 43: After refmac, R = 0.1590 (Rfree = 0.000) for 12334 atoms. Found 141 (141 requested) and removed 150 (141 requested) atoms. Cycle 44: After refmac, R = 0.1564 (Rfree = 0.000) for 12321 atoms. Found 141 (141 requested) and removed 148 (141 requested) atoms. Cycle 45: After refmac, R = 0.1543 (Rfree = 0.000) for 12308 atoms. Found 141 (141 requested) and removed 147 (141 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.16 2.02 NCS extension: 8 residues added (174 deleted due to clashes), 12320 seeds are put forward Round 1: 1310 peptides, 31 chains. Longest chain 114 peptides. Score 0.907 Round 2: 1320 peptides, 28 chains. Longest chain 140 peptides. Score 0.913 Round 3: 1319 peptides, 24 chains. Longest chain 140 peptides. Score 0.917 Round 4: 1316 peptides, 34 chains. Longest chain 139 peptides. Score 0.905 Round 5: 1315 peptides, 31 chains. Longest chain 113 peptides. Score 0.908 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 1295, Estimated correctness of the model 98.8 % 22 chains (1269 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 63 A and 66 A Built loop between residues 156 A and 164 A Built loop between residues 204 A and 207 A Built loop between residues 60 C and 63 C Built loop between residues 64 B and 71 B Built loop between residues 156 B and 164 B Built loop between residues 204 B and 207 B Built loop between residues 101 E and 105 E Built loop between residues 155 E and 163 E Built loop between residues 177 E and 180 E Built loop between residues 156 D and 164 D Built loop between residues 156 F and 162 F Built loop between residues 204 F and 207 F 12 chains (1347 residues) following loop building 9 chains (1323 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 78583 reflections ( 99.94 % complete ) and 11406 restraints for refining 11139 atoms. Observations/parameters ratio is 1.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2463 (Rfree = 0.000) for 11139 atoms. Found 117 (128 requested) and removed 0 (128 requested) atoms. Cycle 47: After refmac, R = 0.2282 (Rfree = 0.000) for 11139 atoms. Found 62 (129 requested) and removed 11 (129 requested) atoms. Cycle 48: After refmac, R = 0.2225 (Rfree = 0.000) for 11139 atoms. Found 27 (130 requested) and removed 11 (130 requested) atoms. Cycle 49: After refmac, R = 0.2196 (Rfree = 0.000) for 11139 atoms. Found 24 (130 requested) and removed 9 (130 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 23:56:31 GMT 2018 Job finished. TimeTaking 268.6 Used memory is bytes: 30383192