Mon 24 Dec 01:04:18 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 2ii1-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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/2ii1-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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 01:04:22 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/2ii1-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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 1083 and 0 Target number of residues in the AU: 1083 Target solvent content: 0.4721 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-1.9-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.50 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 1 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: 91.283 1.950 Wilson plot Bfac: 18.16 70806 reflections ( 90.30 % complete ) and 0 restraints for refining 10697 atoms. Observations/parameters ratio is 1.65 ------------------------------------------------------ Starting model: R = 0.3305 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2779 (Rfree = 0.000) for 10697 atoms. Found 301 (393 requested) and removed 222 (196 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.92 2.17 NCS extension: 0 residues added, 10776 seeds are put forward Round 1: 801 peptides, 107 chains. Longest chain 29 peptides. Score 0.656 Round 2: 927 peptides, 70 chains. Longest chain 51 peptides. Score 0.849 Round 3: 994 peptides, 60 chains. Longest chain 59 peptides. Score 0.892 Round 4: 989 peptides, 55 chains. Longest chain 77 peptides. Score 0.898 Round 5: 1020 peptides, 46 chains. Longest chain 91 peptides. Score 0.920 Taking the results from Round 5 Chains 48, Residues 974, Estimated correctness of the model 99.4 % 23 chains (816 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 87 A Built loop between residues 152 C and 155 C Built loop between residues 214 C and 220 C Built loop between residues 265 C and 270 C Built loop between residues 279 B and 282 B Built loop between residues 212 D and 219 D 42 chains (994 residues) following loop building 17 chains (837 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 11990 restraints for refining 9557 atoms. 5165 conditional restraints added. Observations/parameters ratio is 1.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3053 (Rfree = 0.000) for 9557 atoms. Found 276 (351 requested) and removed 187 (175 requested) atoms. Cycle 2: After refmac, R = 0.2726 (Rfree = 0.000) for 9612 atoms. Found 220 (348 requested) and removed 98 (177 requested) atoms. Cycle 3: After refmac, R = 0.2525 (Rfree = 0.000) for 9665 atoms. Found 190 (351 requested) and removed 57 (179 requested) atoms. Cycle 4: After refmac, R = 0.2385 (Rfree = 0.000) for 9770 atoms. Found 144 (353 requested) and removed 41 (180 requested) atoms. Cycle 5: After refmac, R = 0.2289 (Rfree = 0.000) for 9846 atoms. Found 129 (356 requested) and removed 29 (181 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.90 2.14 NCS extension: 4 residues added (37 deleted due to clashes), 9970 seeds are put forward Round 1: 1023 peptides, 50 chains. Longest chain 78 peptides. Score 0.915 Round 2: 1072 peptides, 30 chains. Longest chain 127 peptides. Score 0.949 Round 3: 1076 peptides, 45 chains. Longest chain 90 peptides. Score 0.932 Round 4: 1076 peptides, 31 chains. Longest chain 128 peptides. Score 0.948 Round 5: 1078 peptides, 40 chains. Longest chain 129 peptides. Score 0.938 Taking the results from Round 2 Chains 32, Residues 1042, Estimated correctness of the model 99.7 % 21 chains (971 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 A and 201 A Built loop between residues 251 A and 256 A Built loop between residues 187 C and 192 C Built loop between residues 213 C and 220 C Built loop between residues 155 D and 159 D Built loop between residues 185 D and 196 D Built loop between residues 214 D and 219 D Built loop between residues 259 D and 263 D Built loop between residues 279 D and 282 D 22 chains (1082 residues) following loop building 12 chains (1012 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10852 restraints for refining 9871 atoms. 2969 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2399 (Rfree = 0.000) for 9871 atoms. Found 265 (356 requested) and removed 178 (181 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 9938 atoms. Found 194 (351 requested) and removed 51 (183 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2108 (Rfree = 0.000) for 10051 atoms. Found 148 (356 requested) and removed 39 (185 requested) atoms. Cycle 9: After refmac, R = 0.2017 (Rfree = 0.000) for 10142 atoms. Found 119 (359 requested) and removed 47 (187 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1955 (Rfree = 0.000) for 10191 atoms. Found 124 (361 requested) and removed 34 (188 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 2.14 NCS extension: 9 residues added (216 deleted due to clashes), 10296 seeds are put forward Round 1: 1068 peptides, 34 chains. Longest chain 90 peptides. Score 0.944 Round 2: 1088 peptides, 31 chains. Longest chain 127 peptides. Score 0.950 Round 3: 1107 peptides, 29 chains. Longest chain 90 peptides. Score 0.954 Round 4: 1106 peptides, 29 chains. Longest chain 137 peptides. Score 0.954 Round 5: 1108 peptides, 30 chains. Longest chain 151 peptides. Score 0.953 Taking the results from Round 4 Chains 30, Residues 1077, Estimated correctness of the model 99.8 % 22 chains (1032 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 122 A Built loop between residues 135 A and 138 A Built loop between residues 149 A and 154 A Built loop between residues 175 A and 178 A Built loop between residues 45 B and 48 B Built loop between residues 61 B and 64 B Built loop between residues 176 B and 179 B Built loop between residues 190 B and 195 B Built loop between residues 216 B and 219 B Built loop between residues 102 D and 113 D Built loop between residues 140 D and 143 D Built loop between residues 151 D and 154 D Built loop between residues 214 D and 219 D 16 chains (1116 residues) following loop building 9 chains (1072 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10549 restraints for refining 10052 atoms. 2297 conditional restraints added. Observations/parameters ratio is 1.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2147 (Rfree = 0.000) for 10052 atoms. Found 298 (355 requested) and removed 156 (185 requested) atoms. Cycle 12: After refmac, R = 0.2008 (Rfree = 0.000) for 10170 atoms. Found 195 (352 requested) and removed 51 (187 requested) atoms. Cycle 13: After refmac, R = 0.1917 (Rfree = 0.000) for 10296 atoms. Found 170 (356 requested) and removed 57 (189 requested) atoms. Cycle 14: After refmac, R = 0.1857 (Rfree = 0.000) for 10393 atoms. Found 156 (360 requested) and removed 51 (191 requested) atoms. Cycle 15: After refmac, R = 0.1813 (Rfree = 0.000) for 10484 atoms. Found 174 (363 requested) and removed 76 (193 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.90 2.14 NCS extension: 19 residues added (225 deleted due to clashes), 10604 seeds are put forward Round 1: 1111 peptides, 32 chains. Longest chain 91 peptides. Score 0.952 Round 2: 1114 peptides, 31 chains. Longest chain 90 peptides. Score 0.953 Round 3: 1118 peptides, 32 chains. Longest chain 91 peptides. Score 0.953 Round 4: 1127 peptides, 26 chains. Longest chain 91 peptides. Score 0.960 Round 5: 1119 peptides, 30 chains. Longest chain 131 peptides. Score 0.955 Taking the results from Round 4 Chains 28, Residues 1101, Estimated correctness of the model 99.8 % 23 chains (1075 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 152 A and 155 A Built loop between residues 186 A and 190 A Built loop between residues 212 A and 219 A Built loop between residues 60 C and 64 C Built loop between residues 153 C and 156 C Built loop between residues 186 C and 189 C Built loop between residues 199 C and 203 C Built loop between residues 216 C and 219 C Built loop between residues 135 B and 138 B Built loop between residues 152 B and 155 B Built loop between residues 186 B and 190 B Built loop between residues 213 B and 219 B Built loop between residues 152 D and 155 D Built loop between residues 174 D and 177 D Built loop between residues 192 D and 195 D Built loop between residues 216 D and 220 D 12 chains (1145 residues) following loop building 7 chains (1119 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10182 restraints for refining 10164 atoms. 1639 conditional restraints added. Observations/parameters ratio is 1.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2035 (Rfree = 0.000) for 10164 atoms. Found 326 (352 requested) and removed 153 (187 requested) atoms. Cycle 17: After refmac, R = 0.1921 (Rfree = 0.000) for 10316 atoms. Found 207 (357 requested) and removed 61 (190 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1833 (Rfree = 0.000) for 10449 atoms. Found 183 (362 requested) and removed 63 (192 requested) atoms. Cycle 19: After refmac, R = 0.1779 (Rfree = 0.000) for 10552 atoms. Found 165 (366 requested) and removed 76 (194 requested) atoms. Cycle 20: After refmac, R = 0.1739 (Rfree = 0.000) for 10625 atoms. Found 153 (368 requested) and removed 86 (195 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 2.14 NCS extension: 19 residues added (291 deleted due to clashes), 10714 seeds are put forward Round 1: 1123 peptides, 29 chains. Longest chain 90 peptides. Score 0.956 Round 2: 1137 peptides, 26 chains. Longest chain 154 peptides. Score 0.961 Round 3: 1125 peptides, 26 chains. Longest chain 131 peptides. Score 0.959 Round 4: 1147 peptides, 24 chains. Longest chain 155 peptides. Score 0.964 Round 5: 1136 peptides, 26 chains. Longest chain 122 peptides. Score 0.961 Taking the results from Round 4 Chains 25, Residues 1123, Estimated correctness of the model 99.9 % 22 chains (1111 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 135 A and 138 A Built loop between residues 151 A and 154 A Built loop between residues 193 A and 197 A Built loop between residues 215 A and 218 A Built loop between residues 278 A and 281 A Built loop between residues 135 C and 138 C Built loop between residues 151 C and 154 C Built loop between residues 193 C and 196 C Built loop between residues 216 C and 219 C Built loop between residues 217 B and 220 B Built loop between residues 278 B and 281 B Built loop between residues 61 D and 65 D Built loop between residues 110 D and 113 D Built loop between residues 152 D and 155 D Built loop between residues 216 D and 219 D 8 chains (1156 residues) following loop building 6 chains (1145 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10107 restraints for refining 10286 atoms. 1412 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1950 (Rfree = 0.000) for 10286 atoms. Found 307 (348 requested) and removed 159 (189 requested) atoms. Cycle 22: After refmac, R = 0.1839 (Rfree = 0.000) for 10407 atoms. Found 209 (346 requested) and removed 67 (192 requested) atoms. Cycle 23: After refmac, R = 0.1764 (Rfree = 0.000) for 10538 atoms. Found 167 (349 requested) and removed 64 (194 requested) atoms. Cycle 24: After refmac, R = 0.1725 (Rfree = 0.000) for 10622 atoms. Found 145 (352 requested) and removed 68 (195 requested) atoms. Cycle 25: After refmac, R = 0.1697 (Rfree = 0.000) for 10688 atoms. Found 148 (354 requested) and removed 68 (196 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.90 2.14 NCS extension: 17 residues added (297 deleted due to clashes), 10789 seeds are put forward Round 1: 1123 peptides, 26 chains. Longest chain 91 peptides. Score 0.959 Round 2: 1129 peptides, 25 chains. Longest chain 154 peptides. Score 0.961 Round 3: 1133 peptides, 29 chains. Longest chain 131 peptides. Score 0.957 Round 4: 1141 peptides, 25 chains. Longest chain 124 peptides. Score 0.962 Round 5: 1149 peptides, 24 chains. Longest chain 131 peptides. Score 0.964 Taking the results from Round 5 Chains 26, Residues 1125, Estimated correctness of the model 99.9 % 21 chains (1104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 216 A and 219 A Built loop between residues 61 C and 64 C Built loop between residues 193 C and 196 C Built loop between residues 216 C and 219 C Built loop between residues 278 C and 281 C Built loop between residues 152 B and 155 B Built loop between residues 174 B and 177 B Built loop between residues 217 B and 224 B Built loop between residues 110 D and 113 D Built loop between residues 140 D and 143 D Built loop between residues 152 D and 155 D Built loop between residues 192 D and 195 D Built loop between residues 215 D and 219 D 11 chains (1154 residues) following loop building 7 chains (1137 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10230 restraints for refining 10301 atoms. 1568 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1898 (Rfree = 0.000) for 10301 atoms. Found 324 (341 requested) and removed 143 (189 requested) atoms. Cycle 27: After refmac, R = 0.1795 (Rfree = 0.000) for 10458 atoms. Found 190 (346 requested) and removed 58 (192 requested) atoms. Cycle 28: After refmac, R = 0.1736 (Rfree = 0.000) for 10577 atoms. Found 168 (350 requested) and removed 70 (194 requested) atoms. Cycle 29: After refmac, R = 0.1691 (Rfree = 0.000) for 10659 atoms. Found 150 (354 requested) and removed 76 (196 requested) atoms. Cycle 30: After refmac, R = 0.1668 (Rfree = 0.000) for 10712 atoms. Found 169 (348 requested) and removed 86 (197 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.89 2.13 NCS extension: 11 residues added (215 deleted due to clashes), 10809 seeds are put forward Round 1: 1130 peptides, 24 chains. Longest chain 91 peptides. Score 0.962 Round 2: 1134 peptides, 25 chains. Longest chain 94 peptides. Score 0.961 Round 3: 1138 peptides, 28 chains. Longest chain 91 peptides. Score 0.959 Round 4: 1147 peptides, 23 chains. Longest chain 119 peptides. Score 0.965 Round 5: 1139 peptides, 28 chains. Longest chain 132 peptides. Score 0.959 Taking the results from Round 4 Chains 24, Residues 1124, Estimated correctness of the model 99.9 % 19 chains (1096 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 C and 64 C Built loop between residues 113 C and 116 C Built loop between residues 193 C and 196 C Built loop between residues 189 B and 195 B Built loop between residues 216 B and 219 B Built loop between residues 153 D and 156 D Built loop between residues 190 D and 193 D Built loop between residues 278 D and 281 D 16 chains (1144 residues) following loop building 11 chains (1116 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10596 restraints for refining 10309 atoms. 2068 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1879 (Rfree = 0.000) for 10309 atoms. Found 312 (326 requested) and removed 137 (189 requested) atoms. Cycle 32: After refmac, R = 0.1778 (Rfree = 0.000) for 10454 atoms. Found 198 (332 requested) and removed 52 (193 requested) atoms. Cycle 33: After refmac, R = 0.1711 (Rfree = 0.000) for 10590 atoms. Found 169 (335 requested) and removed 57 (195 requested) atoms. Cycle 34: After refmac, R = 0.1669 (Rfree = 0.000) for 10688 atoms. Found 162 (339 requested) and removed 70 (197 requested) atoms. Cycle 35: After refmac, R = 0.1648 (Rfree = 0.000) for 10764 atoms. Found 162 (341 requested) and removed 77 (198 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.90 2.14 NCS extension: 2 residues added (169 deleted due to clashes), 10852 seeds are put forward Round 1: 1136 peptides, 25 chains. Longest chain 91 peptides. Score 0.962 Round 2: 1129 peptides, 32 chains. Longest chain 81 peptides. Score 0.954 Round 3: 1125 peptides, 28 chains. Longest chain 127 peptides. Score 0.958 Round 4: 1133 peptides, 27 chains. Longest chain 90 peptides. Score 0.959 Round 5: 1132 peptides, 32 chains. Longest chain 96 peptides. Score 0.954 Taking the results from Round 1 Chains 25, Residues 1111, Estimated correctness of the model 99.8 % 22 chains (1098 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 140 A and 143 A Built loop between residues 151 A and 154 A Built loop between residues 190 A and 195 A Built loop between residues 216 A and 219 A Built loop between residues 60 C and 64 C Built loop between residues 152 C and 155 C Built loop between residues 189 C and 195 C Built loop between residues 215 C and 219 C Built loop between residues 152 B and 155 B Built loop between residues 193 B and 197 B Built loop between residues 216 B and 220 B Built loop between residues 61 D and 64 D Built loop between residues 140 D and 143 D Built loop between residues 152 D and 155 D Built loop between residues 186 D and 195 D Built loop between residues 216 D and 219 D 9 chains (1158 residues) following loop building 6 chains (1145 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10294 restraints for refining 10379 atoms. 1600 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1859 (Rfree = 0.000) for 10379 atoms. Found 329 (329 requested) and removed 127 (191 requested) atoms. Cycle 37: After refmac, R = 0.1761 (Rfree = 0.000) for 10554 atoms. Found 231 (335 requested) and removed 76 (194 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1699 (Rfree = 0.000) for 10691 atoms. Found 178 (339 requested) and removed 82 (197 requested) atoms. Cycle 39: After refmac, R = 0.1657 (Rfree = 0.000) for 10777 atoms. Found 169 (341 requested) and removed 83 (198 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1637 (Rfree = 0.000) for 10844 atoms. Found 175 (343 requested) and removed 100 (199 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.90 2.14 NCS extension: 12 residues added (109 deleted due to clashes), 10936 seeds are put forward Round 1: 1119 peptides, 28 chains. Longest chain 90 peptides. Score 0.957 Round 2: 1140 peptides, 24 chains. Longest chain 128 peptides. Score 0.963 Round 3: 1136 peptides, 31 chains. Longest chain 93 peptides. Score 0.956 Round 4: 1138 peptides, 27 chains. Longest chain 91 peptides. Score 0.960 Round 5: 1146 peptides, 23 chains. Longest chain 131 peptides. Score 0.965 Taking the results from Round 5 Chains 24, Residues 1123, Estimated correctness of the model 99.9 % 19 chains (1095 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 64 A Built loop between residues 152 A and 155 A Built loop between residues 60 C and 64 C Built loop between residues 193 C and 196 C Built loop between residues 216 C and 220 C Built loop between residues 152 B and 155 B Built loop between residues 278 B and 281 B Built loop between residues 155 D and 158 D Built loop between residues 199 D and 203 D Built loop between residues 216 D and 219 D 13 chains (1146 residues) following loop building 9 chains (1119 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10578 restraints for refining 10343 atoms. 2027 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1861 (Rfree = 0.000) for 10343 atoms. Found 319 (319 requested) and removed 120 (190 requested) atoms. Cycle 42: After refmac, R = 0.1744 (Rfree = 0.000) for 10517 atoms. Found 239 (326 requested) and removed 58 (194 requested) atoms. Cycle 43: After refmac, R = 0.1672 (Rfree = 0.000) for 10688 atoms. Found 192 (330 requested) and removed 67 (196 requested) atoms. Cycle 44: After refmac, R = 0.1631 (Rfree = 0.000) for 10801 atoms. Found 174 (334 requested) and removed 96 (199 requested) atoms. Cycle 45: After refmac, R = 0.1603 (Rfree = 0.000) for 10863 atoms. Found 173 (328 requested) and removed 91 (200 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.90 2.14 NCS extension: 8 residues added (209 deleted due to clashes), 10956 seeds are put forward Round 1: 1124 peptides, 27 chains. Longest chain 90 peptides. Score 0.958 Round 2: 1141 peptides, 24 chains. Longest chain 154 peptides. Score 0.963 Round 3: 1140 peptides, 28 chains. Longest chain 127 peptides. Score 0.959 Round 4: 1145 peptides, 22 chains. Longest chain 138 peptides. Score 0.965 Round 5: 1137 peptides, 26 chains. Longest chain 90 peptides. Score 0.961 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 1123, Estimated correctness of the model 99.9 % 19 chains (1110 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 51 A and 64 A Built loop between residues 140 A and 144 A Built loop between residues 190 A and 203 A Built loop between residues 216 A and 219 A Built loop between residues 60 C and 64 C Built loop between residues 152 C and 155 C Built loop between residues 193 C and 196 C Built loop between residues 216 C and 219 C Built loop between residues 200 B and 203 B Built loop between residues 216 B and 219 B Built loop between residues 61 D and 64 D Built loop between residues 140 D and 143 D Built loop between residues 186 D and 190 D Built loop between residues 216 D and 219 D 6 chains (1165 residues) following loop building 5 chains (1161 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. Failed to save intermediate PDB 70806 reflections ( 90.30 % complete ) and 8790 restraints for refining 8647 atoms. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 8647 atoms. Found 174 (254 requested) and removed 0 (254 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2273 (Rfree = 0.000) for 8647 atoms. Found 80 (259 requested) and removed 0 (162 requested) atoms. Cycle 48: After refmac, R = 0.2131 (Rfree = 0.000) for 8647 atoms. Found 28 (262 requested) and removed 6 (163 requested) atoms. Cycle 49: After refmac, R = 0.2103 (Rfree = 0.000) for 8647 atoms. Found 18 (262 requested) and removed 2 (164 requested) atoms. Writing output files ... TimeTaking 116.18