Mon 24 Dec 08:08:04 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 1vkn-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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/1vkn-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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 08:08:08 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/1vkn-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-2.5-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 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-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-2.5-parrot-noncs.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 12504 atoms. Observations/parameters ratio is 1.05 ------------------------------------------------------ Starting model: R = 0.3083 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2236 (Rfree = 0.000) for 12504 atoms. Found 177 (240 requested) and removed 142 (120 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.48 2.55 NCS extension: 0 residues added, 12539 seeds are put forward Round 1: 846 peptides, 122 chains. Longest chain 21 peptides. Score 0.558 Round 2: 976 peptides, 95 chains. Longest chain 49 peptides. Score 0.737 Round 3: 1050 peptides, 82 chains. Longest chain 46 peptides. Score 0.804 Round 4: 1081 peptides, 66 chains. Longest chain 82 peptides. Score 0.848 Round 5: 1113 peptides, 64 chains. Longest chain 96 peptides. Score 0.862 Taking the results from Round 5 Chains 74, Residues 1049, Estimated correctness of the model 96.4 % 25 chains (755 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 45 A and 48 A Built loop between residues 69 A and 73 A Built loop between residues 26 C and 28 C Built loop between residues 226 C and 229 C Built loop between residues 57 B and 60 B Built loop between residues 116 B and 122 B Built loop between residues 133 B and 138 B Built loop between residues 164 B and 168 B Built loop between residues 191 B and 200 B 60 chains (1073 residues) following loop building 15 chains (787 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 13730 restraints for refining 10559 atoms. 6320 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2558 (Rfree = 0.000) for 10559 atoms. Found 202 (202 requested) and removed 119 (101 requested) atoms. Cycle 2: After refmac, R = 0.2295 (Rfree = 0.000) for 10542 atoms. Found 153 (200 requested) and removed 109 (102 requested) atoms. Cycle 3: After refmac, R = 0.2187 (Rfree = 0.000) for 10532 atoms. Found 129 (195 requested) and removed 103 (101 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2110 (Rfree = 0.000) for 10530 atoms. Found 111 (190 requested) and removed 105 (101 requested) atoms. Cycle 5: After refmac, R = 0.2083 (Rfree = 0.000) for 10505 atoms. Found 108 (186 requested) and removed 105 (101 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.49 2.56 NCS extension: 446 residues added (877 deleted due to clashes), 10991 seeds are put forward Round 1: 1133 peptides, 49 chains. Longest chain 107 peptides. Score 0.891 Round 2: 1157 peptides, 43 chains. Longest chain 73 peptides. Score 0.905 Round 3: 1151 peptides, 47 chains. Longest chain 90 peptides. Score 0.898 Round 4: 1119 peptides, 54 chains. Longest chain 115 peptides. Score 0.880 Round 5: 1118 peptides, 54 chains. Longest chain 60 peptides. Score 0.879 Taking the results from Round 2 Chains 47, Residues 1114, Estimated correctness of the model 98.2 % 23 chains (955 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 256 A and 259 A Built loop between residues 306 C and 313 C Built loop between residues 61 B and 64 B Built loop between residues 190 B and 199 B Built loop between residues 308 B and 311 B Built loop between residues 332 B and 335 B Built loop between residues 126 D and 130 D Built loop between residues 257 D and 260 D Built loop between residues 292 D and 295 D Built loop between residues 325 D and 332 D 33 chains (1141 residues) following loop building 13 chains (990 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 12128 restraints for refining 10554 atoms. 3599 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2255 (Rfree = 0.000) for 10554 atoms. Found 182 (182 requested) and removed 117 (101 requested) atoms. Cycle 7: After refmac, R = 0.2031 (Rfree = 0.000) for 10578 atoms. Found 117 (180 requested) and removed 105 (102 requested) atoms. Cycle 8: After refmac, R = 0.1985 (Rfree = 0.000) for 10575 atoms. Found 106 (175 requested) and removed 106 (101 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1893 (Rfree = 0.000) for 10564 atoms. Found 102 (171 requested) and removed 103 (101 requested) atoms. Cycle 10: After refmac, R = 0.1863 (Rfree = 0.000) for 10550 atoms. Found 96 (166 requested) and removed 103 (101 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.49 2.56 NCS extension: 308 residues added (890 deleted due to clashes), 10872 seeds are put forward Round 1: 1152 peptides, 42 chains. Longest chain 75 peptides. Score 0.905 Round 2: 1168 peptides, 43 chains. Longest chain 95 peptides. Score 0.907 Round 3: 1158 peptides, 51 chains. Longest chain 62 peptides. Score 0.894 Round 4: 1164 peptides, 49 chains. Longest chain 89 peptides. Score 0.898 Round 5: 1151 peptides, 54 chains. Longest chain 80 peptides. Score 0.888 Taking the results from Round 2 Chains 47, Residues 1125, Estimated correctness of the model 98.2 % 24 chains (968 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 C and 82 C Built loop between residues 229 C and 232 C Built loop between residues 292 C and 295 C Built loop between residues 323 C and 328 C Built loop between residues 60 B and 63 B Built loop between residues 292 B and 295 B Built loop between residues 307 B and 310 B Built loop between residues 332 B and 335 B Built loop between residues 262 D and 265 D Built loop between residues 291 D and 294 D 36 chains (1145 residues) following loop building 14 chains (990 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 12001 restraints for refining 10554 atoms. 3459 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2064 (Rfree = 0.000) for 10554 atoms. Found 162 (162 requested) and removed 106 (101 requested) atoms. Cycle 12: After refmac, R = 0.1926 (Rfree = 0.000) for 10592 atoms. Found 112 (158 requested) and removed 103 (101 requested) atoms. Cycle 13: After refmac, R = 0.1871 (Rfree = 0.000) for 10590 atoms. Found 105 (154 requested) and removed 104 (101 requested) atoms. Cycle 14: After refmac, R = 0.1834 (Rfree = 0.000) for 10587 atoms. Found 91 (150 requested) and removed 107 (101 requested) atoms. Cycle 15: After refmac, R = 0.1825 (Rfree = 0.000) for 10567 atoms. Found 93 (146 requested) and removed 103 (101 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.50 2.57 NCS extension: 149 residues added (328 deleted due to clashes), 10728 seeds are put forward Round 1: 1156 peptides, 39 chains. Longest chain 115 peptides. Score 0.910 Round 2: 1171 peptides, 37 chains. Longest chain 114 peptides. Score 0.916 Round 3: 1161 peptides, 42 chains. Longest chain 95 peptides. Score 0.907 Round 4: 1136 peptides, 56 chains. Longest chain 65 peptides. Score 0.881 Round 5: 1128 peptides, 48 chains. Longest chain 95 peptides. Score 0.891 Taking the results from Round 2 Chains 42, Residues 1134, Estimated correctness of the model 98.5 % 24 chains (1024 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 226 A and 229 A Built loop between residues 292 A and 295 A Built loop between residues 307 A and 310 A Built loop between residues 92 C and 100 C Built loop between residues 122 C and 126 C Built loop between residues 189 C and 199 C Built loop between residues 271 C and 274 C Built loop between residues 291 C and 294 C Built loop between residues 189 B and 200 B Built loop between residues 212 B and 216 B Built loop between residues 230 B and 237 B Built loop between residues 261 B and 265 B Built loop between residues 228 D and 232 D Built loop between residues 271 D and 274 D Built loop between residues 289 D and 294 D 24 chains (1191 residues) following loop building 9 chains (1084 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11710 restraints for refining 10679 atoms. 2566 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2091 (Rfree = 0.000) for 10679 atoms. Found 143 (143 requested) and removed 115 (102 requested) atoms. Cycle 17: After refmac, R = 0.1908 (Rfree = 0.000) for 10689 atoms. Found 139 (139 requested) and removed 104 (102 requested) atoms. Cycle 18: After refmac, R = 0.1835 (Rfree = 0.000) for 10710 atoms. Found 121 (136 requested) and removed 105 (103 requested) atoms. Cycle 19: After refmac, R = 0.1802 (Rfree = 0.000) for 10723 atoms. Found 106 (132 requested) and removed 107 (103 requested) atoms. Cycle 20: After refmac, R = 0.1771 (Rfree = 0.000) for 10717 atoms. Found 112 (127 requested) and removed 103 (102 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.50 2.57 NCS extension: 446 residues added (482 deleted due to clashes), 11195 seeds are put forward Round 1: 1172 peptides, 36 chains. Longest chain 125 peptides. Score 0.917 Round 2: 1182 peptides, 35 chains. Longest chain 138 peptides. Score 0.920 Round 3: 1184 peptides, 37 chains. Longest chain 91 peptides. Score 0.918 Round 4: 1146 peptides, 48 chains. Longest chain 103 peptides. Score 0.895 Round 5: 1167 peptides, 51 chains. Longest chain 91 peptides. Score 0.896 Taking the results from Round 2 Chains 36, Residues 1147, Estimated correctness of the model 98.7 % 20 chains (1009 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 211 A and 215 A Built loop between residues 228 A and 232 A Built loop between residues 126 C and 136 C Built loop between residues 292 C and 295 C Built loop between residues 281 B and 284 B Built loop between residues 122 D and 125 D 28 chains (1162 residues) following loop building 14 chains (1030 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 12054 restraints for refining 10559 atoms. 3195 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2038 (Rfree = 0.000) for 10559 atoms. Found 121 (121 requested) and removed 113 (101 requested) atoms. Cycle 22: After refmac, R = 0.1878 (Rfree = 0.000) for 10553 atoms. Found 118 (118 requested) and removed 101 (101 requested) atoms. Cycle 23: After refmac, R = 0.1807 (Rfree = 0.000) for 10565 atoms. Found 114 (114 requested) and removed 104 (101 requested) atoms. Cycle 24: After refmac, R = 0.1772 (Rfree = 0.000) for 10570 atoms. Found 107 (110 requested) and removed 101 (101 requested) atoms. Cycle 25: After refmac, R = 0.1748 (Rfree = 0.000) for 10574 atoms. Found 106 (106 requested) and removed 108 (101 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.50 2.57 NCS extension: 164 residues added (996 deleted due to clashes), 10749 seeds are put forward Round 1: 1169 peptides, 39 chains. Longest chain 128 peptides. Score 0.913 Round 2: 1185 peptides, 33 chains. Longest chain 180 peptides. Score 0.923 Round 3: 1181 peptides, 42 chains. Longest chain 122 peptides. Score 0.911 Round 4: 1168 peptides, 43 chains. Longest chain 76 peptides. Score 0.907 Round 5: 1155 peptides, 48 chains. Longest chain 101 peptides. Score 0.897 Taking the results from Round 2 Chains 36, Residues 1152, Estimated correctness of the model 98.8 % 24 chains (1077 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 133 A Built loop between residues 190 A and 200 A Built loop between residues 229 A and 232 A Built loop between residues 323 A and 328 A Built loop between residues 212 C and 216 C Built loop between residues 273 C and 276 C Built loop between residues 43 B and 48 B Built loop between residues 92 B and 99 B Built loop between residues 226 B and 229 B Built loop between residues 292 B and 295 B Built loop between residues 292 D and 295 D 24 chains (1197 residues) following loop building 13 chains (1123 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11486 restraints for refining 10674 atoms. 2162 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2056 (Rfree = 0.000) for 10674 atoms. Found 102 (102 requested) and removed 118 (102 requested) atoms. Cycle 27: After refmac, R = 0.1886 (Rfree = 0.000) for 10645 atoms. Found 102 (102 requested) and removed 103 (102 requested) atoms. Cycle 28: After refmac, R = 0.1806 (Rfree = 0.000) for 10637 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1769 (Rfree = 0.000) for 10633 atoms. Found 102 (102 requested) and removed 106 (102 requested) atoms. Cycle 30: After refmac, R = 0.1751 (Rfree = 0.000) for 10625 atoms. Found 93 (102 requested) and removed 106 (102 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.50 2.57 NCS extension: 308 residues added (1047 deleted due to clashes), 10932 seeds are put forward Round 1: 1181 peptides, 43 chains. Longest chain 101 peptides. Score 0.910 Round 2: 1185 peptides, 31 chains. Longest chain 133 peptides. Score 0.926 Round 3: 1180 peptides, 41 chains. Longest chain 88 peptides. Score 0.912 Round 4: 1172 peptides, 44 chains. Longest chain 93 peptides. Score 0.907 Round 5: 1170 peptides, 41 chains. Longest chain 117 peptides. Score 0.910 Taking the results from Round 2 Chains 34, Residues 1154, Estimated correctness of the model 98.8 % 21 chains (1074 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 278 A and 281 A Built loop between residues 126 C and 129 C Built loop between residues 328 C and 331 C Built loop between residues 127 B and 138 B Built loop between residues 153 B and 156 B Built loop between residues 226 B and 229 B Built loop between residues 94 D and 100 D Built loop between residues 229 D and 233 D Built loop between residues 272 D and 275 D Built loop between residues 291 D and 294 D 23 chains (1183 residues) following loop building 11 chains (1106 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11477 restraints for refining 10554 atoms. 2283 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1986 (Rfree = 0.000) for 10554 atoms. Found 101 (101 requested) and removed 111 (101 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1836 (Rfree = 0.000) for 10537 atoms. Found 101 (101 requested) and removed 103 (101 requested) atoms. Cycle 33: After refmac, R = 0.1773 (Rfree = 0.000) for 10532 atoms. Found 101 (101 requested) and removed 103 (101 requested) atoms. Cycle 34: After refmac, R = 0.1747 (Rfree = 0.000) for 10529 atoms. Found 101 (101 requested) and removed 102 (101 requested) atoms. Cycle 35: After refmac, R = 0.1737 (Rfree = 0.000) for 10524 atoms. Found 101 (101 requested) and removed 106 (101 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.49 2.56 NCS extension: 135 residues added (340 deleted due to clashes), 10665 seeds are put forward Round 1: 1172 peptides, 31 chains. Longest chain 122 peptides. Score 0.923 Round 2: 1184 peptides, 34 chains. Longest chain 117 peptides. Score 0.922 Round 3: 1181 peptides, 33 chains. Longest chain 123 peptides. Score 0.922 Round 4: 1170 peptides, 39 chains. Longest chain 73 peptides. Score 0.913 Round 5: 1156 peptides, 47 chains. Longest chain 119 peptides. Score 0.899 Taking the results from Round 1 Chains 33, Residues 1141, Estimated correctness of the model 98.8 % 24 chains (1075 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 133 A Built loop between residues 292 A and 295 A Built loop between residues 323 A and 334 A Built loop between residues 93 C and 99 C Built loop between residues 135 C and 139 C Built loop between residues 230 C and 233 C Built loop between residues 242 C and 245 C Built loop between residues 291 C and 294 C Built loop between residues 323 C and 328 C Built loop between residues 24 B and 30 B Built loop between residues 169 B and 175 B Built loop between residues 126 D and 131 D Built loop between residues 190 D and 200 D 18 chains (1195 residues) following loop building 11 chains (1138 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11546 restraints for refining 10703 atoms. 2168 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2025 (Rfree = 0.000) for 10703 atoms. Found 102 (102 requested) and removed 112 (102 requested) atoms. Cycle 37: After refmac, R = 0.1853 (Rfree = 0.000) for 10681 atoms. Found 102 (102 requested) and removed 105 (102 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1775 (Rfree = 0.000) for 10675 atoms. Found 102 (102 requested) and removed 105 (102 requested) atoms. Cycle 39: After refmac, R = 0.1744 (Rfree = 0.000) for 10670 atoms. Found 102 (102 requested) and removed 106 (102 requested) atoms. Cycle 40: After refmac, R = 0.1728 (Rfree = 0.000) for 10666 atoms. Found 102 (102 requested) and removed 106 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.50 2.57 NCS extension: 398 residues added (1119 deleted due to clashes), 11070 seeds are put forward Round 1: 1184 peptides, 34 chains. Longest chain 128 peptides. Score 0.922 Round 2: 1188 peptides, 34 chains. Longest chain 118 peptides. Score 0.923 Round 3: 1188 peptides, 32 chains. Longest chain 117 peptides. Score 0.925 Round 4: 1170 peptides, 39 chains. Longest chain 82 peptides. Score 0.913 Round 5: 1154 peptides, 47 chains. Longest chain 61 peptides. Score 0.899 Taking the results from Round 3 Chains 37, Residues 1156, Estimated correctness of the model 98.8 % 23 chains (1087 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 174 A Built loop between residues 212 A and 216 A Built loop between residues 260 A and 263 A Built loop between residues 92 C and 100 C Built loop between residues 134 C and 140 C Built loop between residues 292 C and 295 C Built loop between residues 73 B and 80 B Built loop between residues 91 B and 100 B Built loop between residues 114 B and 117 B Built loop between residues 308 B and 311 B Built loop between residues 128 D and 131 D Built loop between residues 190 D and 200 D Built loop between residues 246 D and 249 D 22 chains (1205 residues) following loop building 10 chains (1141 residues) in sequence following loop building ------------------------------------------------------ 52490 reflections ( 98.47 % complete ) and 11500 restraints for refining 10735 atoms. 2059 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2066 (Rfree = 0.000) for 10735 atoms. Found 103 (103 requested) and removed 120 (103 requested) atoms. Cycle 42: After refmac, R = 0.1882 (Rfree = 0.000) for 10709 atoms. Found 102 (102 requested) and removed 102 (102 requested) atoms. Cycle 43: After refmac, R = 0.1814 (Rfree = 0.000) for 10704 atoms. Found 102 (102 requested) and removed 104 (102 requested) atoms. Cycle 44: After refmac, R = 0.1785 (Rfree = 0.000) for 10700 atoms. Found 102 (102 requested) and removed 106 (102 requested) atoms. Cycle 45: After refmac, R = 0.1765 (Rfree = 0.000) for 10692 atoms. Found 102 (102 requested) and removed 102 (102 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.51 2.58 NCS extension: 301 residues added (1090 deleted due to clashes), 11006 seeds are put forward Round 1: 1169 peptides, 35 chains. Longest chain 110 peptides. Score 0.918 Round 2: 1186 peptides, 34 chains. Longest chain 177 peptides. Score 0.922 Round 3: 1184 peptides, 40 chains. Longest chain 91 peptides. Score 0.914 Round 4: 1172 peptides, 43 chains. Longest chain 97 peptides. Score 0.908 Round 5: 1158 peptides, 45 chains. Longest chain 117 peptides. Score 0.902 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 1152, Estimated correctness of the model 98.7 % 23 chains (1075 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 136 A and 139 A Built loop between residues 158 A and 161 A Built loop between residues 189 A and 200 A Built loop between residues 292 A and 295 A Built loop between residues 71 C and 81 C Built loop between residues 94 C and 100 C Built loop between residues 190 C and 200 C Built loop between residues 230 C and 233 C Built loop between residues 292 C and 295 C Built loop between residues 169 B and 175 B Built loop between residues 261 B and 270 B Built loop between residues 188 D and 197 D Built loop between residues 265 D and 268 D Built loop between residues 291 D and 294 D 19 chains (1212 residues) following loop building 9 chains (1143 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 52490 reflections ( 98.47 % complete ) and 9452 restraints for refining 9264 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2721 (Rfree = 0.000) for 9264 atoms. Found 75 (88 requested) and removed 0 (88 requested) atoms. Cycle 47: After refmac, R = 0.2529 (Rfree = 0.000) for 9264 atoms. Found 29 (89 requested) and removed 2 (89 requested) atoms. Cycle 48: After refmac, R = 0.2453 (Rfree = 0.000) for 9264 atoms. Found 16 (89 requested) and removed 6 (89 requested) atoms. Cycle 49: After refmac, R = 0.2417 (Rfree = 0.000) for 9264 atoms. TimeTaking 135.52