null Mon 24 Dec 01:05:36 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 1vkd-2.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-2.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-2.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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/1vkd-2.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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 01:05:40 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/1vkd-2.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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 1921 and 0 Target number of residues in the AU: 1921 Target solvent content: 0.5377 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-2.6-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: 19 Cell parameters: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-2.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 16224 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. 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: 127.440 2.600 Wilson plot Bfac: 32.25 69678 reflections ( 99.15 % complete ) and 0 restraints for refining 17907 atoms. Observations/parameters ratio is 0.97 ------------------------------------------------------ Starting model: R = 0.2891 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1969 (Rfree = 0.000) for 17907 atoms. Found 290 (290 requested) and removed 160 (145 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.44 2.41 NCS extension: 0 residues added, 18037 seeds are put forward Round 1: 1448 peptides, 183 chains. Longest chain 38 peptides. Score 0.645 Round 2: 1635 peptides, 116 chains. Longest chain 97 peptides. Score 0.824 Round 3: 1722 peptides, 87 chains. Longest chain 99 peptides. Score 0.876 Round 4: 1777 peptides, 78 chains. Longest chain 96 peptides. Score 0.894 Round 5: 1811 peptides, 59 chains. Longest chain 130 peptides. Score 0.916 Taking the results from Round 5 Chains 66, Residues 1752, Estimated correctness of the model 98.2 % 40 chains (1578 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 61 A and 68 A Built loop between residues 135 A and 138 A Built loop between residues 184 A and 193 A Built loop between residues 312 A and 316 A Built loop between residues 64 C and 71 C Built loop between residues 108 C and 111 C Built loop between residues 184 C and 193 C Built loop between residues 233 C and 236 C Built loop between residues 270 C and 274 C Built loop between residues 42 B and 51 B Built loop between residues 63 B and 66 B Built loop between residues 90 B and 94 B Built loop between residues 214 B and 217 B Built loop between residues 115 E and 122 E Built loop between residues 233 E and 236 E Built loop between residues 264 E and 267 E Built loop between residues 106 D and 111 D Built loop between residues 135 D and 138 D Built loop between residues 169 D and 172 D Built loop between residues 42 F and 47 F Built loop between residues 63 F and 66 F Built loop between residues 88 F and 92 F Built loop between residues 138 F and 141 F Built loop between residues 155 F and 159 F Built loop between residues 297 F and 300 F 35 chains (1836 residues) following loop building 14 chains (1671 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 14586 restraints for refining 17062 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2459 (Rfree = 0.000) for 17062 atoms. Found 276 (276 requested) and removed 207 (138 requested) atoms. Cycle 2: After refmac, R = 0.2046 (Rfree = 0.000) for 17131 atoms. Found 271 (271 requested) and removed 160 (138 requested) atoms. Cycle 3: After refmac, R = 0.1887 (Rfree = 0.000) for 17242 atoms. Found 170 (268 requested) and removed 158 (139 requested) atoms. Cycle 4: After refmac, R = 0.1787 (Rfree = 0.000) for 17254 atoms. Found 177 (262 requested) and removed 154 (139 requested) atoms. Cycle 5: After refmac, R = 0.1717 (Rfree = 0.000) for 17277 atoms. Found 181 (258 requested) and removed 158 (140 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.44 2.41 NCS extension: 61 residues added (295 deleted due to clashes), 17411 seeds are put forward Round 1: 1837 peptides, 50 chains. Longest chain 146 peptides. Score 0.926 Round 2: 1855 peptides, 37 chains. Longest chain 146 peptides. Score 0.938 Round 3: 1852 peptides, 45 chains. Longest chain 140 peptides. Score 0.931 Round 4: 1854 peptides, 45 chains. Longest chain 147 peptides. Score 0.932 Round 5: 1848 peptides, 48 chains. Longest chain 148 peptides. Score 0.929 Taking the results from Round 2 Chains 41, Residues 1818, Estimated correctness of the model 99.0 % 29 chains (1737 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 46 A Built loop between residues 183 A and 193 A Built loop between residues 305 A and 308 A Built loop between residues 313 A and 317 A Built loop between residues 136 C and 139 C Built loop between residues 184 C and 194 C Built loop between residues 136 B and 139 B Built loop between residues 183 B and 193 B Built loop between residues 42 E and 47 E Built loop between residues 160 E and 164 E Built loop between residues 28 D and 31 D Built loop between residues 41 D and 47 D Built loop between residues 182 D and 193 D Built loop between residues 57 F and 60 F Built loop between residues 107 F and 111 F Built loop between residues 160 F and 163 F Built loop between residues 214 F and 217 F 23 chains (1889 residues) following loop building 12 chains (1810 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15497 restraints for refining 16876 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2099 (Rfree = 0.000) for 16876 atoms. Found 246 (246 requested) and removed 195 (136 requested) atoms. Cycle 7: After refmac, R = 0.1807 (Rfree = 0.000) for 16927 atoms. Found 241 (241 requested) and removed 146 (137 requested) atoms. Cycle 8: After refmac, R = 0.1694 (Rfree = 0.000) for 17022 atoms. Found 237 (237 requested) and removed 146 (138 requested) atoms. Cycle 9: After refmac, R = 0.1615 (Rfree = 0.000) for 17113 atoms. Found 205 (233 requested) and removed 165 (138 requested) atoms. Cycle 10: After refmac, R = 0.1563 (Rfree = 0.000) for 17153 atoms. Found 223 (228 requested) and removed 155 (139 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.44 2.41 NCS extension: 733 residues added (1834 deleted due to clashes), 17983 seeds are put forward Round 1: 1860 peptides, 40 chains. Longest chain 149 peptides. Score 0.936 Round 2: 1861 peptides, 34 chains. Longest chain 146 peptides. Score 0.940 Round 3: 1867 peptides, 38 chains. Longest chain 122 peptides. Score 0.938 Round 4: 1862 peptides, 43 chains. Longest chain 148 peptides. Score 0.934 Round 5: 1850 peptides, 50 chains. Longest chain 137 peptides. Score 0.927 Taking the results from Round 2 Chains 39, Residues 1827, Estimated correctness of the model 99.0 % 28 chains (1651 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 182 A and 190 A Built loop between residues 288 A and 292 A Built loop between residues 314 A and 317 A Built loop between residues 136 C and 139 C Built loop between residues 183 C and 193 C Built loop between residues 136 B and 139 B Built loop between residues 184 B and 193 B Built loop between residues 265 B and 268 B Built loop between residues 282 B and 285 B Built loop between residues 304 B and 307 B Built loop between residues 136 E and 139 E Built loop between residues 182 E and 193 E Built loop between residues 63 F and 67 F Built loop between residues 264 F and 267 F 23 chains (1887 residues) following loop building 13 chains (1712 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15076 restraints for refining 16657 atoms. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1948 (Rfree = 0.000) for 16657 atoms. Found 216 (216 requested) and removed 166 (135 requested) atoms. Cycle 12: After refmac, R = 0.1697 (Rfree = 0.000) for 16707 atoms. Found 211 (211 requested) and removed 142 (135 requested) atoms. Cycle 13: After refmac, R = 0.1597 (Rfree = 0.000) for 16776 atoms. Found 207 (207 requested) and removed 140 (136 requested) atoms. Cycle 14: After refmac, R = 0.1539 (Rfree = 0.000) for 16843 atoms. Found 200 (202 requested) and removed 146 (136 requested) atoms. Cycle 15: After refmac, R = 0.1502 (Rfree = 0.000) for 16897 atoms. Found 197 (197 requested) and removed 146 (137 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.43 2.40 NCS extension: 94 residues added (869 deleted due to clashes), 17059 seeds are put forward Round 1: 1858 peptides, 39 chains. Longest chain 146 peptides. Score 0.936 Round 2: 1879 peptides, 34 chains. Longest chain 146 peptides. Score 0.942 Round 3: 1883 peptides, 34 chains. Longest chain 150 peptides. Score 0.942 Round 4: 1862 peptides, 40 chains. Longest chain 138 peptides. Score 0.936 Round 5: 1866 peptides, 44 chains. Longest chain 149 peptides. Score 0.934 Taking the results from Round 3 Chains 39, Residues 1849, Estimated correctness of the model 99.1 % 30 chains (1798 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A Built loop between residues 136 A and 139 A Built loop between residues 171 A and 175 A Built loop between residues 185 A and 193 A Built loop between residues 64 C and 67 C Built loop between residues 130 C and 136 C Built loop between residues 282 C and 285 C Built loop between residues 42 B and 47 B Built loop between residues 63 B and 66 B Built loop between residues 183 B and 188 B Built loop between residues 42 E and 47 E Built loop between residues 134 E and 137 E Built loop between residues 160 E and 163 E Built loop between residues 183 E and 193 E Built loop between residues 41 D and 47 D Built loop between residues 191 D and 194 D Built loop between residues 41 F and 47 F Built loop between residues 136 F and 139 F Built loop between residues 147 F and 150 F Built loop between residues 182 F and 193 F Built loop between residues 227 F and 230 F Built loop between residues 315 F and 318 F 15 chains (1923 residues) following loop building 8 chains (1878 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15894 restraints for refining 16819 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1836 (Rfree = 0.000) for 16819 atoms. Found 190 (190 requested) and removed 182 (136 requested) atoms. Cycle 17: After refmac, R = 0.1617 (Rfree = 0.000) for 16827 atoms. Found 185 (185 requested) and removed 161 (136 requested) atoms. Cycle 18: After refmac, R = 0.1525 (Rfree = 0.000) for 16851 atoms. Found 180 (180 requested) and removed 157 (136 requested) atoms. Cycle 19: After refmac, R = 0.1474 (Rfree = 0.000) for 16874 atoms. Found 175 (175 requested) and removed 142 (136 requested) atoms. Cycle 20: After refmac, R = 0.1441 (Rfree = 0.000) for 16907 atoms. Found 170 (170 requested) and removed 140 (137 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.43 2.40 NCS extension: 31 residues added (689 deleted due to clashes), 17004 seeds are put forward Round 1: 1873 peptides, 45 chains. Longest chain 146 peptides. Score 0.934 Round 2: 1877 peptides, 34 chains. Longest chain 149 peptides. Score 0.942 Round 3: 1876 peptides, 38 chains. Longest chain 144 peptides. Score 0.939 Round 4: 1863 peptides, 41 chains. Longest chain 144 peptides. Score 0.935 Round 5: 1863 peptides, 44 chains. Longest chain 149 peptides. Score 0.933 Taking the results from Round 2 Chains 41, Residues 1843, Estimated correctness of the model 99.1 % 31 chains (1808 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 136 A and 139 A Built loop between residues 185 A and 193 A Built loop between residues 281 A and 288 A Built loop between residues 315 A and 318 A Built loop between residues 40 C and 47 C Built loop between residues 63 C and 67 C Built loop between residues 136 C and 139 C Built loop between residues 161 C and 164 C Built loop between residues 184 C and 193 C Built loop between residues 137 B and 140 B Built loop between residues 183 B and 193 B Built loop between residues 214 B and 217 B Built loop between residues 42 E and 47 E Built loop between residues 185 E and 189 E Built loop between residues 265 E and 268 E Built loop between residues 315 E and 318 E Built loop between residues 42 D and 47 D Built loop between residues 148 D and 151 D Built loop between residues 185 D and 188 D Built loop between residues 40 F and 44 F Built loop between residues 111 F and 114 F Built loop between residues 135 F and 138 F Built loop between residues 182 F and 193 F 13 chains (1926 residues) following loop building 7 chains (1899 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 16020 restraints for refining 16800 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1746 (Rfree = 0.000) for 16800 atoms. Found 163 (163 requested) and removed 166 (136 requested) atoms. Cycle 22: After refmac, R = 0.1560 (Rfree = 0.000) for 16797 atoms. Found 158 (158 requested) and removed 144 (136 requested) atoms. Cycle 23: After refmac, R = 0.1496 (Rfree = 0.000) for 16811 atoms. Found 152 (152 requested) and removed 146 (136 requested) atoms. Cycle 24: After refmac, R = 0.1467 (Rfree = 0.000) for 16817 atoms. Found 147 (147 requested) and removed 143 (136 requested) atoms. Cycle 25: After refmac, R = 0.1452 (Rfree = 0.000) for 16821 atoms. Found 141 (141 requested) and removed 140 (136 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.43 2.40 NCS extension: 14 residues added (965 deleted due to clashes), 16867 seeds are put forward Round 1: 1873 peptides, 43 chains. Longest chain 146 peptides. Score 0.935 Round 2: 1884 peptides, 31 chains. Longest chain 151 peptides. Score 0.945 Round 3: 1888 peptides, 33 chains. Longest chain 149 peptides. Score 0.943 Round 4: 1876 peptides, 43 chains. Longest chain 149 peptides. Score 0.935 Round 5: 1879 peptides, 44 chains. Longest chain 146 peptides. Score 0.935 Taking the results from Round 2 Chains 36, Residues 1853, Estimated correctness of the model 99.2 % 26 chains (1802 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 185 A and 188 A Built loop between residues 136 B and 139 B Built loop between residues 185 B and 189 B Built loop between residues 185 E and 193 E Built loop between residues 265 E and 268 E Built loop between residues 305 E and 308 E Built loop between residues 63 D and 66 D Built loop between residues 136 D and 139 D Built loop between residues 183 D and 189 D Built loop between residues 226 D and 229 D Built loop between residues 65 F and 73 F Built loop between residues 183 F and 191 F Built loop between residues 315 F and 318 F 22 chains (1903 residues) following loop building 12 chains (1852 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15718 restraints for refining 16691 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1687 (Rfree = 0.000) for 16691 atoms. Found 135 (135 requested) and removed 155 (135 requested) atoms. Cycle 27: After refmac, R = 0.1555 (Rfree = 0.000) for 16671 atoms. Found 135 (135 requested) and removed 138 (135 requested) atoms. Cycle 28: After refmac, R = 0.1504 (Rfree = 0.000) for 16668 atoms. Found 135 (135 requested) and removed 142 (135 requested) atoms. Cycle 29: After refmac, R = 0.1477 (Rfree = 0.000) for 16661 atoms. Found 135 (135 requested) and removed 139 (135 requested) atoms. Cycle 30: After refmac, R = 0.1468 (Rfree = 0.000) for 16657 atoms. Found 135 (135 requested) and removed 142 (135 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.43 2.40 NCS extension: 24 residues added (554 deleted due to clashes), 16698 seeds are put forward Round 1: 1870 peptides, 41 chains. Longest chain 147 peptides. Score 0.936 Round 2: 1892 peptides, 29 chains. Longest chain 149 peptides. Score 0.947 Round 3: 1882 peptides, 37 chains. Longest chain 144 peptides. Score 0.940 Round 4: 1881 peptides, 38 chains. Longest chain 146 peptides. Score 0.939 Round 5: 1880 peptides, 41 chains. Longest chain 140 peptides. Score 0.937 Taking the results from Round 2 Chains 32, Residues 1863, Estimated correctness of the model 99.2 % 25 chains (1827 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 185 A and 190 A Built loop between residues 42 C and 47 C Built loop between residues 136 C and 139 C Built loop between residues 184 C and 193 C Built loop between residues 42 B and 47 B Built loop between residues 185 B and 193 B Built loop between residues 265 B and 268 B Built loop between residues 41 E and 47 E Built loop between residues 148 E and 151 E Built loop between residues 184 D and 193 D Built loop between residues 30 F and 33 F Built loop between residues 63 F and 67 F Built loop between residues 227 F and 230 F Built loop between residues 264 F and 267 F 16 chains (1919 residues) following loop building 10 chains (1887 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15951 restraints for refining 16722 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1694 (Rfree = 0.000) for 16722 atoms. Found 135 (135 requested) and removed 163 (135 requested) atoms. Cycle 32: After refmac, R = 0.1534 (Rfree = 0.000) for 16694 atoms. Found 135 (135 requested) and removed 146 (135 requested) atoms. Cycle 33: After refmac, R = 0.1485 (Rfree = 0.000) for 16683 atoms. Found 135 (135 requested) and removed 139 (135 requested) atoms. Cycle 34: After refmac, R = 0.1455 (Rfree = 0.000) for 16679 atoms. Found 135 (135 requested) and removed 142 (135 requested) atoms. Cycle 35: After refmac, R = 0.1452 (Rfree = 0.000) for 16672 atoms. Found 135 (135 requested) and removed 139 (135 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.43 2.40 NCS extension: 16 residues added (846 deleted due to clashes), 16716 seeds are put forward Round 1: 1865 peptides, 45 chains. Longest chain 147 peptides. Score 0.933 Round 2: 1877 peptides, 33 chains. Longest chain 149 peptides. Score 0.942 Round 3: 1856 peptides, 45 chains. Longest chain 147 peptides. Score 0.932 Round 4: 1873 peptides, 38 chains. Longest chain 145 peptides. Score 0.939 Round 5: 1852 peptides, 52 chains. Longest chain 119 peptides. Score 0.926 Taking the results from Round 2 Chains 43, Residues 1844, Estimated correctness of the model 99.1 % 32 chains (1819 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 185 A and 193 A Built loop between residues 285 A and 288 A Built loop between residues 315 A and 318 A Built loop between residues 30 C and 33 C Built loop between residues 105 C and 110 C Built loop between residues 136 C and 139 C Built loop between residues 147 C and 150 C Built loop between residues 214 C and 217 C Built loop between residues 265 C and 268 C Built loop between residues 305 C and 308 C Built loop between residues 42 B and 47 B Built loop between residues 148 B and 151 B Built loop between residues 185 B and 190 B Built loop between residues 41 E and 47 E Built loop between residues 185 E and 193 E Built loop between residues 184 D and 193 D Built loop between residues 214 D and 217 D Built loop between residues 65 F and 68 F Built loop between residues 136 F and 139 F Built loop between residues 183 F and 193 F Built loop between residues 315 F and 318 F 21 chains (1916 residues) following loop building 11 chains (1893 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15978 restraints for refining 16765 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1675 (Rfree = 0.000) for 16765 atoms. Found 135 (135 requested) and removed 159 (135 requested) atoms. Cycle 37: After refmac, R = 0.1515 (Rfree = 0.000) for 16741 atoms. Found 135 (135 requested) and removed 139 (135 requested) atoms. Cycle 38: After refmac, R = 0.1467 (Rfree = 0.000) for 16737 atoms. Found 135 (135 requested) and removed 137 (135 requested) atoms. Cycle 39: After refmac, R = 0.1448 (Rfree = 0.000) for 16735 atoms. Found 135 (135 requested) and removed 140 (135 requested) atoms. Cycle 40: After refmac, R = 0.1441 (Rfree = 0.000) for 16730 atoms. Found 135 (135 requested) and removed 136 (135 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.43 2.40 NCS extension: 24 residues added (425 deleted due to clashes), 16777 seeds are put forward Round 1: 1858 peptides, 46 chains. Longest chain 146 peptides. Score 0.931 Round 2: 1884 peptides, 31 chains. Longest chain 146 peptides. Score 0.945 Round 3: 1885 peptides, 37 chains. Longest chain 147 peptides. Score 0.940 Round 4: 1864 peptides, 42 chains. Longest chain 146 peptides. Score 0.935 Round 5: 1874 peptides, 42 chains. Longest chain 144 peptides. Score 0.936 Taking the results from Round 2 Chains 34, Residues 1853, Estimated correctness of the model 99.2 % 29 chains (1832 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 135 A and 138 A Built loop between residues 185 A and 189 A Built loop between residues 285 A and 288 A Built loop between residues 265 C and 268 C Built loop between residues 41 B and 47 B Built loop between residues 184 B and 193 B Built loop between residues 40 E and 49 E Built loop between residues 136 E and 139 E Built loop between residues 147 E and 150 E Built loop between residues 182 E and 190 E Built loop between residues 214 E and 217 E Built loop between residues 42 D and 47 D Built loop between residues 124 D and 127 D Built loop between residues 185 D and 190 D Built loop between residues 265 D and 268 D Built loop between residues 315 D and 318 D Built loop between residues 30 F and 33 F Built loop between residues 41 F and 47 F Built loop between residues 136 F and 139 F Built loop between residues 184 F and 193 F 13 chains (1932 residues) following loop building 8 chains (1911 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 16101 restraints for refining 16795 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1692 (Rfree = 0.000) for 16795 atoms. Found 136 (136 requested) and removed 164 (136 requested) atoms. Cycle 42: After refmac, R = 0.1525 (Rfree = 0.000) for 16767 atoms. Found 135 (135 requested) and removed 146 (135 requested) atoms. Cycle 43: After refmac, R = 0.1476 (Rfree = 0.000) for 16756 atoms. Found 135 (135 requested) and removed 144 (135 requested) atoms. Cycle 44: After refmac, R = 0.1451 (Rfree = 0.000) for 16747 atoms. Found 135 (135 requested) and removed 137 (135 requested) atoms. Cycle 45: After refmac, R = 0.1437 (Rfree = 0.000) for 16745 atoms. Found 135 (135 requested) and removed 142 (135 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.41 NCS extension: 23 residues added (520 deleted due to clashes), 16786 seeds are put forward Round 1: 1868 peptides, 42 chains. Longest chain 146 peptides. Score 0.935 Round 2: 1882 peptides, 28 chains. Longest chain 149 peptides. Score 0.946 Round 3: 1876 peptides, 40 chains. Longest chain 146 peptides. Score 0.937 Round 4: 1883 peptides, 37 chains. Longest chain 140 peptides. Score 0.940 Round 5: 1885 peptides, 36 chains. Longest chain 146 peptides. Score 0.941 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 1854, Estimated correctness of the model 99.2 % 27 chains (1840 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 185 A and 193 A Built loop between residues 315 A and 318 A Built loop between residues 29 C and 33 C Built loop between residues 136 C and 139 C Built loop between residues 147 C and 150 C Built loop between residues 184 C and 193 C Built loop between residues 136 B and 139 B Built loop between residues 183 B and 193 B Built loop between residues 30 E and 33 E Built loop between residues 42 E and 49 E Built loop between residues 136 E and 139 E Built loop between residues 41 D and 47 D Built loop between residues 185 D and 188 D Built loop between residues 42 F and 47 F Built loop between residues 185 F and 192 F Built loop between residues 227 F and 230 F Built loop between residues 264 F and 267 F 13 chains (1923 residues) following loop building 9 chains (1911 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 69678 reflections ( 99.15 % complete ) and 16079 restraints for refining 15551 atoms. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2221 (Rfree = 0.000) for 15551 atoms. Found 126 (126 requested) and removed 0 (126 requested) atoms. Cycle 47: After refmac, R = 0.2053 (Rfree = 0.000) for 15551 atoms. Found 127 (127 requested) and removed 10 (127 requested) atoms. Cycle 48: After refmac, R = 0.1951 (Rfree = 0.000) for 15551 atoms. Found 81 (128 requested) and removed 14 (128 requested) atoms. Cycle 49: After refmac, R = 0.1909 (Rfree = 0.000) for 15551 atoms. Found 46 (128 requested) and removed 14 (128 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 05:09:51 GMT 2018 Job finished. TimeTaking 244.26 Used memory is bytes: 16220096