null Tue 25 Dec 19:27:57 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 1vkd-2.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-2.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-2.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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/1vkd-2.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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 19:28:07 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/1vkd-2.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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 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-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: 19 Cell parameters: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-2.6-parrot-hancs.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 18017 atoms. Observations/parameters ratio is 0.97 ------------------------------------------------------ Starting model: R = 0.2894 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1982 (Rfree = 0.000) for 18017 atoms. Found 249 (292 requested) and removed 160 (146 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.43 2.40 NCS extension: 0 residues added, 18106 seeds are put forward Round 1: 1416 peptides, 184 chains. Longest chain 34 peptides. Score 0.628 Round 2: 1612 peptides, 122 chains. Longest chain 73 peptides. Score 0.810 Round 3: 1727 peptides, 94 chains. Longest chain 82 peptides. Score 0.870 Round 4: 1777 peptides, 63 chains. Longest chain 113 peptides. Score 0.908 Round 5: 1798 peptides, 62 chains. Longest chain 101 peptides. Score 0.912 Taking the results from Round 5 Chains 66, Residues 1736, Estimated correctness of the model 98.1 % 40 chains (1550 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 67 A Built loop between residues 92 A and 95 A Built loop between residues 137 A and 141 A Built loop between residues 288 A and 291 A Built loop between residues 105 C and 108 C Built loop between residues 267 C and 278 C Built loop between residues 292 C and 295 C Built loop between residues 64 B and 71 B Built loop between residues 136 B and 139 B Built loop between residues 146 B and 149 B Built loop between residues 182 B and 193 B Built loop between residues 228 B and 232 B Built loop between residues 161 E and 171 E Built loop between residues 227 E and 230 E Built loop between residues 305 E and 310 E Built loop between residues 42 D and 47 D Built loop between residues 106 D and 109 D Built loop between residues 147 D and 152 D Built loop between residues 185 D and 193 D Built loop between residues 292 D and 295 D Built loop between residues 90 F and 93 F Built loop between residues 108 F and 111 F Built loop between residues 160 F and 163 F Built loop between residues 305 F and 308 F 39 chains (1809 residues) following loop building 16 chains (1638 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 14375 restraints for refining 17168 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2401 (Rfree = 0.000) for 17168 atoms. Found 278 (278 requested) and removed 205 (139 requested) atoms. Cycle 2: After refmac, R = 0.2084 (Rfree = 0.000) for 17241 atoms. Found 261 (273 requested) and removed 162 (139 requested) atoms. Cycle 3: After refmac, R = 0.1892 (Rfree = 0.000) for 17340 atoms. Found 194 (270 requested) and removed 163 (140 requested) atoms. Cycle 4: After refmac, R = 0.1790 (Rfree = 0.000) for 17371 atoms. Found 144 (264 requested) and removed 153 (140 requested) atoms. Cycle 5: After refmac, R = 0.1746 (Rfree = 0.000) for 17362 atoms. Found 136 (259 requested) and removed 146 (140 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.44 2.41 NCS extension: 54 residues added (326 deleted due to clashes), 17456 seeds are put forward Round 1: 1837 peptides, 42 chains. Longest chain 145 peptides. Score 0.932 Round 2: 1859 peptides, 36 chains. Longest chain 146 peptides. Score 0.939 Round 3: 1842 peptides, 48 chains. Longest chain 132 peptides. Score 0.928 Round 4: 1854 peptides, 47 chains. Longest chain 109 peptides. Score 0.930 Round 5: 1837 peptides, 47 chains. Longest chain 147 peptides. Score 0.928 Taking the results from Round 2 Chains 40, Residues 1823, Estimated correctness of the model 99.0 % 29 chains (1750 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 33 A Built loop between residues 42 A and 47 A Built loop between residues 63 A and 67 A Built loop between residues 136 A and 139 A Built loop between residues 183 A and 190 A Built loop between residues 265 A and 268 A Built loop between residues 39 C and 48 C Built loop between residues 57 C and 60 C Built loop between residues 136 C and 139 C Built loop between residues 183 C and 193 C Built loop between residues 265 C and 268 C Built loop between residues 41 B and 46 B Built loop between residues 184 B and 193 B Built loop between residues 315 B and 318 B Built loop between residues 42 E and 47 E Built loop between residues 63 E and 66 E Built loop between residues 211 E and 214 E Built loop between residues 41 D and 47 D Built loop between residues 186 D and 191 D Built loop between residues 105 F and 108 F Built loop between residues 135 F and 138 F Built loop between residues 182 F and 193 F 15 chains (1907 residues) following loop building 7 chains (1838 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15650 restraints for refining 16970 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2054 (Rfree = 0.000) for 16970 atoms. Found 247 (247 requested) and removed 190 (137 requested) atoms. Cycle 7: After refmac, R = 0.1747 (Rfree = 0.000) for 17027 atoms. Found 243 (243 requested) and removed 156 (138 requested) atoms. Cycle 8: After refmac, R = 0.1633 (Rfree = 0.000) for 17114 atoms. Found 238 (238 requested) and removed 150 (138 requested) atoms. Cycle 9: After refmac, R = 0.1571 (Rfree = 0.000) for 17202 atoms. Found 213 (234 requested) and removed 156 (139 requested) atoms. Cycle 10: After refmac, R = 0.1523 (Rfree = 0.000) for 17259 atoms. Found 207 (229 requested) and removed 147 (139 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.43 2.40 NCS extension: 87 residues added (1221 deleted due to clashes), 17438 seeds are put forward Round 1: 1874 peptides, 42 chains. Longest chain 146 peptides. Score 0.936 Round 2: 1875 peptides, 32 chains. Longest chain 148 peptides. Score 0.943 Round 3: 1872 peptides, 36 chains. Longest chain 146 peptides. Score 0.940 Round 4: 1865 peptides, 36 chains. Longest chain 145 peptides. Score 0.939 Round 5: 1880 peptides, 36 chains. Longest chain 151 peptides. Score 0.941 Taking the results from Round 2 Chains 35, Residues 1843, Estimated correctness of the model 99.1 % 27 chains (1803 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 161 A and 164 A Built loop between residues 171 A and 175 A Built loop between residues 185 A and 191 A Built loop between residues 136 C and 139 C Built loop between residues 147 C and 150 C Built loop between residues 226 C and 229 C Built loop between residues 136 B and 139 B Built loop between residues 185 B and 193 B Built loop between residues 265 B and 268 B Built loop between residues 315 B and 318 B Built loop between residues 315 E and 318 E Built loop between residues 40 D and 47 D Built loop between residues 185 D and 193 D 19 chains (1887 residues) following loop building 13 chains (1851 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15675 restraints for refining 16747 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1821 (Rfree = 0.000) for 16747 atoms. Found 217 (217 requested) and removed 163 (135 requested) atoms. Cycle 12: After refmac, R = 0.1594 (Rfree = 0.000) for 16801 atoms. Found 212 (212 requested) and removed 145 (136 requested) atoms. Cycle 13: After refmac, R = 0.1518 (Rfree = 0.000) for 16868 atoms. Found 207 (207 requested) and removed 149 (136 requested) atoms. Cycle 14: After refmac, R = 0.1477 (Rfree = 0.000) for 16926 atoms. Found 203 (203 requested) and removed 142 (137 requested) atoms. Cycle 15: After refmac, R = 0.1461 (Rfree = 0.000) for 16987 atoms. Found 198 (198 requested) and removed 141 (137 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.43 2.40 NCS extension: 35 residues added (701 deleted due to clashes), 17096 seeds are put forward Round 1: 1870 peptides, 35 chains. Longest chain 145 peptides. Score 0.940 Round 2: 1885 peptides, 33 chains. Longest chain 150 peptides. Score 0.943 Round 3: 1878 peptides, 38 chains. Longest chain 150 peptides. Score 0.939 Round 4: 1872 peptides, 43 chains. Longest chain 150 peptides. Score 0.935 Round 5: 1865 peptides, 47 chains. Longest chain 128 peptides. Score 0.931 Taking the results from Round 2 Chains 38, Residues 1852, Estimated correctness of the model 99.1 % 30 chains (1825 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 123 A and 126 A Built loop between residues 185 A and 190 A Built loop between residues 265 A and 268 A Built loop between residues 315 A and 318 A Built loop between residues 137 C and 140 C Built loop between residues 41 B and 47 B Built loop between residues 136 B and 139 B Built loop between residues 182 B and 193 B Built loop between residues 315 B and 318 B Built loop between residues 324 B and 327 B Built loop between residues 41 E and 47 E Built loop between residues 136 D and 139 D Built loop between residues 185 D and 188 D Built loop between residues 315 D and 318 D Built loop between residues 29 F and 34 F Built loop between residues 42 F and 47 F Built loop between residues 135 F and 139 F Built loop between residues 185 F and 193 F Built loop between residues 315 F and 318 F 16 chains (1918 residues) following loop building 10 chains (1893 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15992 restraints for refining 16857 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1802 (Rfree = 0.000) for 16857 atoms. Found 191 (191 requested) and removed 166 (136 requested) atoms. Cycle 17: After refmac, R = 0.1580 (Rfree = 0.000) for 16882 atoms. Found 186 (186 requested) and removed 145 (136 requested) atoms. Cycle 18: After refmac, R = 0.1494 (Rfree = 0.000) for 16923 atoms. Found 181 (181 requested) and removed 149 (137 requested) atoms. Cycle 19: After refmac, R = 0.1457 (Rfree = 0.000) for 16955 atoms. Found 175 (175 requested) and removed 150 (137 requested) atoms. Cycle 20: After refmac, R = 0.1434 (Rfree = 0.000) for 16980 atoms. Found 170 (170 requested) and removed 140 (137 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.43 2.40 NCS extension: 37 residues added (992 deleted due to clashes), 17065 seeds are put forward Round 1: 1876 peptides, 42 chains. Longest chain 125 peptides. Score 0.936 Round 2: 1883 peptides, 28 chains. Longest chain 151 peptides. Score 0.946 Round 3: 1872 peptides, 41 chains. Longest chain 147 peptides. Score 0.936 Round 4: 1884 peptides, 31 chains. Longest chain 145 peptides. Score 0.945 Round 5: 1864 peptides, 45 chains. Longest chain 143 peptides. Score 0.933 Taking the results from Round 2 Chains 32, Residues 1855, Estimated correctness of the model 99.2 % 24 chains (1728 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 41 C and 47 C Built loop between residues 183 C and 192 C Built loop between residues 260 C and 263 C Built loop between residues 42 B and 47 B Built loop between residues 181 B and 189 B Built loop between residues 42 E and 47 E Built loop between residues 315 E and 318 E Built loop between residues 185 D and 193 D Built loop between residues 265 D and 268 D Built loop between residues 214 F and 217 F 20 chains (1907 residues) following loop building 12 chains (1780 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15423 restraints for refining 16731 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1725 (Rfree = 0.000) for 16731 atoms. Found 163 (163 requested) and removed 153 (135 requested) atoms. Cycle 22: After refmac, R = 0.1575 (Rfree = 0.000) for 16741 atoms. Found 157 (157 requested) and removed 139 (135 requested) atoms. Cycle 23: After refmac, R = 0.1519 (Rfree = 0.000) for 16759 atoms. Found 152 (152 requested) and removed 146 (135 requested) atoms. Cycle 24: After refmac, R = 0.1490 (Rfree = 0.000) for 16765 atoms. Found 146 (146 requested) and removed 141 (135 requested) atoms. Cycle 25: After refmac, R = 0.1480 (Rfree = 0.000) for 16770 atoms. Found 141 (141 requested) and removed 138 (135 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.43 2.40 NCS extension: 16 residues added (347 deleted due to clashes), 16812 seeds are put forward Round 1: 1862 peptides, 43 chains. Longest chain 124 peptides. Score 0.934 Round 2: 1884 peptides, 27 chains. Longest chain 151 peptides. Score 0.947 Round 3: 1872 peptides, 43 chains. Longest chain 136 peptides. Score 0.935 Round 4: 1871 peptides, 36 chains. Longest chain 144 peptides. Score 0.940 Round 5: 1862 peptides, 44 chains. Longest chain 136 peptides. Score 0.933 Taking the results from Round 2 Chains 33, Residues 1857, Estimated correctness of the model 99.2 % 27 chains (1845 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A 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 41 C and 47 C Built loop between residues 185 C and 193 C Built loop between residues 135 B and 138 B Built loop between residues 185 B and 188 B Built loop between residues 29 E and 35 E Built loop between residues 105 E and 108 E Built loop between residues 135 E and 138 E Built loop between residues 226 E and 229 E Built loop between residues 136 D and 139 D Built loop between residues 185 D and 193 D Built loop between residues 170 F and 175 F Built loop between residues 186 F and 193 F 16 chains (1915 residues) following loop building 11 chains (1906 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 16031 restraints for refining 16783 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1696 (Rfree = 0.000) for 16783 atoms. Found 136 (136 requested) and removed 160 (136 requested) atoms. Cycle 27: After refmac, R = 0.1546 (Rfree = 0.000) for 16759 atoms. Found 135 (135 requested) and removed 148 (135 requested) atoms. Cycle 28: After refmac, R = 0.1481 (Rfree = 0.000) for 16746 atoms. Found 135 (135 requested) and removed 143 (135 requested) atoms. Cycle 29: After refmac, R = 0.1462 (Rfree = 0.000) for 16738 atoms. Found 135 (135 requested) and removed 136 (135 requested) atoms. Cycle 30: After refmac, R = 0.1444 (Rfree = 0.000) for 16737 atoms. Found 135 (135 requested) and removed 136 (135 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.43 2.40 NCS extension: 23 residues added (686 deleted due to clashes), 16773 seeds are put forward Round 1: 1860 peptides, 38 chains. Longest chain 147 peptides. Score 0.937 Round 2: 1877 peptides, 32 chains. Longest chain 146 peptides. Score 0.943 Round 3: 1865 peptides, 41 chains. Longest chain 138 peptides. Score 0.936 Round 4: 1885 peptides, 39 chains. Longest chain 140 peptides. Score 0.939 Round 5: 1874 peptides, 39 chains. Longest chain 145 peptides. Score 0.938 Taking the results from Round 2 Chains 38, Residues 1845, Estimated correctness of the model 99.1 % 31 chains (1821 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 184 A and 193 A Built loop between residues 30 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 214 C and 217 C Built loop between residues 315 C and 318 C Built loop between residues 136 B and 139 B Built loop between residues 185 B and 193 B Built loop between residues 285 B and 288 B Built loop between residues 42 E and 47 E Built loop between residues 285 E and 288 E Built loop between residues 315 E and 318 E Built loop between residues 41 D and 47 D Built loop between residues 135 D and 138 D Built loop between residues 186 D and 193 D Built loop between residues 315 D and 318 D Built loop between residues 170 F and 175 F Built loop between residues 315 F and 318 F 19 chains (1900 residues) following loop building 13 chains (1879 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15849 restraints for refining 16687 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1737 (Rfree = 0.000) for 16687 atoms. Found 135 (135 requested) and removed 156 (135 requested) atoms. Cycle 32: After refmac, R = 0.1558 (Rfree = 0.000) for 16666 atoms. Found 135 (135 requested) and removed 138 (135 requested) atoms. Cycle 33: After refmac, R = 0.1499 (Rfree = 0.000) for 16663 atoms. Found 135 (135 requested) and removed 139 (135 requested) atoms. Cycle 34: After refmac, R = 0.1481 (Rfree = 0.000) for 16659 atoms. Found 135 (135 requested) and removed 141 (135 requested) atoms. Cycle 35: After refmac, R = 0.1461 (Rfree = 0.000) for 16653 atoms. Found 135 (135 requested) and removed 137 (135 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.43 2.40 NCS extension: 36 residues added (768 deleted due to clashes), 16703 seeds are put forward Round 1: 1879 peptides, 38 chains. Longest chain 147 peptides. Score 0.939 Round 2: 1876 peptides, 37 chains. Longest chain 142 peptides. Score 0.940 Round 3: 1869 peptides, 43 chains. Longest chain 144 peptides. Score 0.935 Round 4: 1875 peptides, 36 chains. Longest chain 147 peptides. Score 0.940 Round 5: 1860 peptides, 43 chains. Longest chain 141 peptides. Score 0.934 Taking the results from Round 4 Chains 38, Residues 1839, Estimated correctness of the model 99.0 % 32 chains (1790 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 47 A Built loop between residues 112 A and 115 A Built loop between residues 182 A and 190 A Built loop between residues 205 A and 208 A Built loop between residues 315 A and 318 A Built loop between residues 184 C and 194 C Built loop between residues 265 C and 268 C Built loop between residues 136 B and 139 B Built loop between residues 147 B and 150 B Built loop between residues 185 B and 193 B Built loop between residues 42 E and 47 E Built loop between residues 63 E and 66 E Built loop between residues 233 E and 236 E Built loop between residues 42 D and 47 D Built loop between residues 64 D and 67 D Built loop between residues 214 D and 217 D Built loop between residues 315 D and 318 D Built loop between residues 183 F and 193 F Built loop between residues 261 F and 264 F Built loop between residues 318 F and 321 F 17 chains (1907 residues) following loop building 12 chains (1861 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15769 restraints for refining 16692 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1734 (Rfree = 0.000) for 16692 atoms. Found 135 (135 requested) and removed 167 (135 requested) atoms. Cycle 37: After refmac, R = 0.1561 (Rfree = 0.000) for 16660 atoms. Found 135 (135 requested) and removed 141 (135 requested) atoms. Cycle 38: After refmac, R = 0.1497 (Rfree = 0.000) for 16654 atoms. Found 135 (135 requested) and removed 149 (135 requested) atoms. Cycle 39: After refmac, R = 0.1466 (Rfree = 0.000) for 16640 atoms. Found 134 (134 requested) and removed 139 (134 requested) atoms. Cycle 40: After refmac, R = 0.1456 (Rfree = 0.000) for 16635 atoms. Found 134 (134 requested) and removed 139 (134 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.43 2.40 NCS extension: 49 residues added (1250 deleted due to clashes), 16708 seeds are put forward Round 1: 1859 peptides, 44 chains. Longest chain 146 peptides. Score 0.933 Round 2: 1874 peptides, 35 chains. Longest chain 145 peptides. Score 0.941 Round 3: 1867 peptides, 43 chains. Longest chain 140 peptides. Score 0.934 Round 4: 1860 peptides, 39 chains. Longest chain 140 peptides. Score 0.937 Round 5: 1849 peptides, 48 chains. Longest chain 131 peptides. Score 0.929 Taking the results from Round 2 Chains 43, Residues 1839, Estimated correctness of the model 99.1 % 32 chains (1800 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 135 A and 138 A Built loop between residues 185 A and 188 A Built loop between residues 315 A and 318 A Built loop between residues 148 C and 151 C Built loop between residues 184 C and 193 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 40 B and 47 B Built loop between residues 110 B and 114 B Built loop between residues 136 B and 139 B Built loop between residues 147 B and 150 B Built loop between residues 184 B and 193 B Built loop between residues 214 B and 217 B Built loop between residues 41 E and 47 E Built loop between residues 185 E and 193 E Built loop between residues 315 E and 318 E Built loop between residues 135 D and 138 D Built loop between residues 185 D and 193 D Built loop between residues 285 D and 288 D Built loop between residues 63 F and 67 F Built loop between residues 136 F and 139 F Built loop between residues 185 F and 193 F 18 chains (1923 residues) following loop building 8 chains (1886 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 15951 restraints for refining 16786 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1737 (Rfree = 0.000) for 16786 atoms. Found 136 (136 requested) and removed 175 (136 requested) atoms. Cycle 42: After refmac, R = 0.1550 (Rfree = 0.000) for 16747 atoms. Found 135 (135 requested) and removed 152 (135 requested) atoms. Cycle 43: After refmac, R = 0.1487 (Rfree = 0.000) for 16730 atoms. Found 135 (135 requested) and removed 153 (135 requested) atoms. Cycle 44: After refmac, R = 0.1461 (Rfree = 0.000) for 16712 atoms. Found 135 (135 requested) and removed 137 (135 requested) atoms. Cycle 45: After refmac, R = 0.1447 (Rfree = 0.000) for 16710 atoms. Found 135 (135 requested) and removed 139 (135 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.41 NCS extension: 15 residues added (512 deleted due to clashes), 16752 seeds are put forward Round 1: 1861 peptides, 40 chains. Longest chain 146 peptides. Score 0.936 Round 2: 1869 peptides, 30 chains. Longest chain 146 peptides. Score 0.944 Round 3: 1873 peptides, 42 chains. Longest chain 139 peptides. Score 0.936 Round 4: 1872 peptides, 41 chains. Longest chain 147 peptides. Score 0.936 Round 5: 1857 peptides, 44 chains. Longest chain 139 peptides. Score 0.933 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 1839, Estimated correctness of the model 99.2 % 26 chains (1807 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 42 A and 47 A Built loop between residues 123 A and 126 A Built loop between residues 185 A and 193 A Built loop between residues 282 A and 285 A Built loop between residues 42 C and 47 C Built loop between residues 41 B and 47 B Built loop between residues 41 E and 47 E Built loop between residues 135 E and 138 E Built loop between residues 185 E and 193 E Built loop between residues 63 D and 67 D Built loop between residues 136 D and 139 D Built loop between residues 136 F and 139 F Built loop between residues 147 F and 150 F Built loop between residues 184 F and 193 F Built loop between residues 315 F and 318 F 16 chains (1896 residues) following loop building 11 chains (1864 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 69678 reflections ( 99.15 % complete ) and 15759 restraints for refining 15254 atoms. Observations/parameters ratio is 1.14 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2265 (Rfree = 0.000) for 15254 atoms. Found 123 (123 requested) and removed 0 (123 requested) atoms. Cycle 47: After refmac, R = 0.2108 (Rfree = 0.000) for 15254 atoms. Found 124 (124 requested) and removed 6 (124 requested) atoms. Cycle 48: After refmac, R = 0.2010 (Rfree = 0.000) for 15254 atoms. Found 81 (125 requested) and removed 11 (125 requested) atoms. Cycle 49: After refmac, R = 0.1958 (Rfree = 0.000) for 15254 atoms. Found 53 (126 requested) and removed 20 (126 requested) atoms. Writing output files ... Normal termination of warpNtrace Wed 26 Dec 00:09:36 GMT 2018 Job finished. TimeTaking 281.64 Used memory is bytes: 19690584