null Sun 23 Dec 22:23:02 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 1vkm-2.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-2.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkm-2.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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/1vkm-2.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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 ============================================================ Sun 23 Dec 22:23:11 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/1vkm-2.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkm-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 1469 and 0 Target number of residues in the AU: 1469 Target solvent content: 0.5273 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-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: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-2.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 14256 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 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: 75.160 2.600 Wilson plot Bfac: 29.58 52578 reflections ( 99.99 % complete ) and 0 restraints for refining 15799 atoms. Observations/parameters ratio is 0.83 ------------------------------------------------------ Starting model: R = 0.2891 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1894 (Rfree = 0.000) for 15799 atoms. Found 203 (256 requested) and removed 154 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.64 NCS extension: 0 residues added, 15848 seeds are put forward Round 1: 1205 peptides, 167 chains. Longest chain 25 peptides. Score 0.638 Round 2: 1378 peptides, 114 chains. Longest chain 55 peptides. Score 0.830 Round 3: 1481 peptides, 82 chains. Longest chain 70 peptides. Score 0.897 Round 4: 1547 peptides, 69 chains. Longest chain 145 peptides. Score 0.921 Round 5: 1552 peptides, 68 chains. Longest chain 102 peptides. Score 0.922 Taking the results from Round 5 Chains 72, Residues 1484, Estimated correctness of the model 98.5 % 32 chains (1116 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 133 A and 144 A Built loop between residues 130 C and 136 C Built loop between residues 183 B and 190 B Built loop between residues 66 E and 74 E Built loop between residues 141 E and 144 E Built loop between residues 161 E and 171 E Built loop between residues 19 D and 26 D Built loop between residues 41 D and 45 D Built loop between residues 72 D and 75 D Built loop between residues 98 D and 102 D 59 chains (1527 residues) following loop building 22 chains (1169 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 17472 restraints for refining 14037 atoms. 6869 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2592 (Rfree = 0.000) for 14037 atoms. Found 194 (227 requested) and removed 163 (113 requested) atoms. Cycle 2: After refmac, R = 0.2324 (Rfree = 0.000) for 13898 atoms. Found 143 (223 requested) and removed 119 (114 requested) atoms. Cycle 3: After refmac, R = 0.2231 (Rfree = 0.000) for 13804 atoms. Found 94 (216 requested) and removed 114 (112 requested) atoms. Cycle 4: After refmac, R = 0.2144 (Rfree = 0.000) for 13744 atoms. Found 75 (210 requested) and removed 113 (111 requested) atoms. Cycle 5: After refmac, R = 0.2120 (Rfree = 0.000) for 13678 atoms. Found 67 (204 requested) and removed 111 (111 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.39 2.63 NCS extension: 538 residues added (2086 deleted due to clashes), 14194 seeds are put forward Round 1: 1602 peptides, 50 chains. Longest chain 183 peptides. Score 0.943 Round 2: 1624 peptides, 50 chains. Longest chain 166 peptides. Score 0.945 Round 3: 1610 peptides, 59 chains. Longest chain 101 peptides. Score 0.937 Round 4: 1609 peptides, 62 chains. Longest chain 80 peptides. Score 0.934 Round 5: 1616 peptides, 57 chains. Longest chain 95 peptides. Score 0.939 Taking the results from Round 2 Chains 54, Residues 1574, Estimated correctness of the model 99.2 % 31 chains (1365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 183 A and 186 A Built loop between residues 71 C and 74 C Built loop between residues 132 C and 143 C Built loop between residues 72 B and 76 B Built loop between residues 144 B and 147 B Built loop between residues 72 E and 76 E Built loop between residues 187 E and 190 E Built loop between residues 72 D and 75 D Built loop between residues 114 D and 117 D Built loop between residues 187 D and 190 D Built loop between residues 132 F and 135 F 41 chains (1600 residues) following loop building 20 chains (1397 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 15737 restraints for refining 13860 atoms. 3970 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2268 (Rfree = 0.000) for 13860 atoms. Found 202 (202 requested) and removed 148 (112 requested) atoms. Cycle 7: After refmac, R = 0.2103 (Rfree = 0.000) for 13884 atoms. Found 148 (198 requested) and removed 113 (112 requested) atoms. Cycle 8: After refmac, R = 0.2021 (Rfree = 0.000) for 13891 atoms. Found 116 (193 requested) and removed 115 (112 requested) atoms. Cycle 9: After refmac, R = 0.1974 (Rfree = 0.000) for 13872 atoms. Found 102 (189 requested) and removed 114 (112 requested) atoms. Cycle 10: After refmac, R = 0.1952 (Rfree = 0.000) for 13839 atoms. Found 96 (184 requested) and removed 113 (112 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.38 2.61 NCS extension: 79 residues added (1413 deleted due to clashes), 13912 seeds are put forward Round 1: 1618 peptides, 42 chains. Longest chain 217 peptides. Score 0.951 Round 2: 1626 peptides, 43 chains. Longest chain 155 peptides. Score 0.951 Round 3: 1624 peptides, 49 chains. Longest chain 184 peptides. Score 0.946 Round 4: 1600 peptides, 75 chains. Longest chain 75 peptides. Score 0.922 Round 5: 1613 peptides, 56 chains. Longest chain 140 peptides. Score 0.940 Taking the results from Round 2 Chains 45, Residues 1583, Estimated correctness of the model 99.3 % 31 chains (1478 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 77 A Built loop between residues 133 A and 136 A Built loop between residues 19 C and 26 C Built loop between residues 74 C and 77 C Built loop between residues 132 C and 135 C Built loop between residues 18 B and 22 B Built loop between residues 78 B and 88 B Built loop between residues 119 B and 123 B Built loop between residues 132 B and 135 B Built loop between residues 188 B and 191 B Built loop between residues 42 E and 45 E Built loop between residues 71 E and 74 E Built loop between residues 205 E and 208 E Built loop between residues 190 D and 193 D Built loop between residues 272 D and 276 D Built loop between residues 45 F and 48 F Built loop between residues 140 F and 143 F Built loop between residues 184 F and 190 F Built loop between residues 208 F and 211 F 24 chains (1636 residues) following loop building 12 chains (1533 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14787 restraints for refining 13913 atoms. 2342 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2167 (Rfree = 0.000) for 13913 atoms. Found 180 (180 requested) and removed 142 (112 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 13917 atoms. Found 176 (176 requested) and removed 113 (113 requested) atoms. Cycle 13: After refmac, R = 0.1945 (Rfree = 0.000) for 13962 atoms. Found 146 (172 requested) and removed 114 (113 requested) atoms. Cycle 14: After refmac, R = 0.1887 (Rfree = 0.000) for 13977 atoms. Found 137 (167 requested) and removed 117 (113 requested) atoms. Cycle 15: After refmac, R = 0.1826 (Rfree = 0.000) for 13983 atoms. Found 110 (163 requested) and removed 118 (113 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.40 2.64 NCS extension: 103 residues added (363 deleted due to clashes), 14084 seeds are put forward Round 1: 1641 peptides, 46 chains. Longest chain 117 peptides. Score 0.950 Round 2: 1655 peptides, 38 chains. Longest chain 219 peptides. Score 0.957 Round 3: 1636 peptides, 48 chains. Longest chain 112 peptides. Score 0.948 Round 4: 1634 peptides, 49 chains. Longest chain 184 peptides. Score 0.947 Round 5: 1638 peptides, 52 chains. Longest chain 151 peptides. Score 0.945 Taking the results from Round 2 Chains 43, Residues 1617, Estimated correctness of the model 99.5 % 27 chains (1475 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 218 A and 221 A Built loop between residues 261 C and 272 C Built loop between residues 139 B and 142 B Built loop between residues 212 B and 215 B Built loop between residues 18 E and 22 E Built loop between residues 155 E and 159 E Built loop between residues 171 E and 175 E Built loop between residues 233 E and 236 E Built loop between residues 253 E and 256 E Built loop between residues 267 E and 270 E Built loop between residues 30 D and 33 D Built loop between residues 74 D and 80 D Built loop between residues 194 F and 197 F 26 chains (1650 residues) following loop building 14 chains (1515 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14716 restraints for refining 13869 atoms. 2256 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2056 (Rfree = 0.000) for 13869 atoms. Found 157 (157 requested) and removed 142 (112 requested) atoms. Cycle 17: After refmac, R = 0.1902 (Rfree = 0.000) for 13855 atoms. Found 153 (153 requested) and removed 113 (112 requested) atoms. Cycle 18: After refmac, R = 0.1840 (Rfree = 0.000) for 13885 atoms. Found 109 (148 requested) and removed 113 (112 requested) atoms. Cycle 19: After refmac, R = 0.1794 (Rfree = 0.000) for 13874 atoms. Found 131 (144 requested) and removed 121 (112 requested) atoms. Cycle 20: After refmac, R = 0.1731 (Rfree = 0.000) for 13873 atoms. Found 113 (139 requested) and removed 113 (112 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.40 2.64 NCS extension: 213 residues added (1560 deleted due to clashes), 14097 seeds are put forward Round 1: 1647 peptides, 43 chains. Longest chain 148 peptides. Score 0.953 Round 2: 1647 peptides, 43 chains. Longest chain 124 peptides. Score 0.953 Round 3: 1655 peptides, 40 chains. Longest chain 173 peptides. Score 0.955 Round 4: 1639 peptides, 49 chains. Longest chain 146 peptides. Score 0.948 Round 5: 1649 peptides, 51 chains. Longest chain 150 peptides. Score 0.947 Taking the results from Round 3 Chains 45, Residues 1615, Estimated correctness of the model 99.4 % 31 chains (1516 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 23 A Built loop between residues 140 A and 143 A Built loop between residues 155 A and 158 A Built loop between residues 209 A and 212 A Built loop between residues 19 C and 23 C Built loop between residues 194 C and 197 C Built loop between residues 18 B and 24 B Built loop between residues 145 B and 149 B Built loop between residues 173 B and 176 B Built loop between residues 140 E and 143 E Built loop between residues 194 E and 197 E Built loop between residues 45 D and 48 D Built loop between residues 71 D and 74 D Built loop between residues 114 D and 117 D Built loop between residues 190 D and 194 D Built loop between residues 215 D and 218 D Built loop between residues 78 F and 86 F Built loop between residues 140 F and 145 F Built loop between residues 163 F and 166 F 25 chains (1666 residues) following loop building 12 chains (1568 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14531 restraints for refining 13953 atoms. 1762 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2031 (Rfree = 0.000) for 13953 atoms. Found 136 (136 requested) and removed 137 (113 requested) atoms. Cycle 22: After refmac, R = 0.1889 (Rfree = 0.000) for 13925 atoms. Found 131 (131 requested) and removed 114 (113 requested) atoms. Cycle 23: After refmac, R = 0.1819 (Rfree = 0.000) for 13928 atoms. Found 127 (127 requested) and removed 114 (113 requested) atoms. Cycle 24: After refmac, R = 0.1778 (Rfree = 0.000) for 13935 atoms. Found 122 (122 requested) and removed 120 (113 requested) atoms. Cycle 25: After refmac, R = 0.1753 (Rfree = 0.000) for 13923 atoms. Found 118 (118 requested) and removed 117 (113 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.40 2.64 NCS extension: 24 residues added (279 deleted due to clashes), 13957 seeds are put forward Round 1: 1665 peptides, 34 chains. Longest chain 182 peptides. Score 0.960 Round 2: 1671 peptides, 35 chains. Longest chain 196 peptides. Score 0.960 Round 3: 1658 peptides, 43 chains. Longest chain 141 peptides. Score 0.954 Round 4: 1658 peptides, 44 chains. Longest chain 189 peptides. Score 0.953 Round 5: 1625 peptides, 57 chains. Longest chain 154 peptides. Score 0.940 Taking the results from Round 2 Chains 39, Residues 1636, Estimated correctness of the model 99.5 % 29 chains (1556 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 85 A Built loop between residues 134 A and 137 A Built loop between residues 186 A and 189 A Built loop between residues 234 A and 237 A Built loop between residues 19 C and 22 C Built loop between residues 72 C and 76 C Built loop between residues 270 C and 273 C Built loop between residues 71 B and 74 B Built loop between residues 19 E and 24 E Built loop between residues 92 E and 98 E Built loop between residues 139 E and 142 E Built loop between residues 187 E and 190 E Built loop between residues 64 D and 69 D Built loop between residues 187 D and 190 D Built loop between residues 265 D and 268 D Built loop between residues 21 F and 24 F Built loop between residues 118 F and 121 F Built loop between residues 192 F and 195 F Built loop between residues 211 F and 214 F 18 chains (1684 residues) following loop building 10 chains (1610 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14406 restraints for refining 14015 atoms. 1372 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2063 (Rfree = 0.000) for 14015 atoms. Found 113 (113 requested) and removed 136 (113 requested) atoms. Cycle 27: After refmac, R = 0.1869 (Rfree = 0.000) for 13965 atoms. Found 113 (113 requested) and removed 114 (113 requested) atoms. Cycle 28: After refmac, R = 0.1787 (Rfree = 0.000) for 13955 atoms. Found 113 (113 requested) and removed 120 (113 requested) atoms. Cycle 29: After refmac, R = 0.1738 (Rfree = 0.000) for 13945 atoms. Found 113 (113 requested) and removed 117 (113 requested) atoms. Cycle 30: After refmac, R = 0.1713 (Rfree = 0.000) for 13931 atoms. Found 113 (113 requested) and removed 114 (113 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.40 2.64 NCS extension: 32 residues added (430 deleted due to clashes), 13971 seeds are put forward Round 1: 1672 peptides, 27 chains. Longest chain 203 peptides. Score 0.965 Round 2: 1665 peptides, 35 chains. Longest chain 112 peptides. Score 0.960 Round 3: 1674 peptides, 33 chains. Longest chain 153 peptides. Score 0.962 Round 4: 1654 peptides, 51 chains. Longest chain 140 peptides. Score 0.947 Round 5: 1651 peptides, 43 chains. Longest chain 162 peptides. Score 0.953 Taking the results from Round 1 Chains 29, Residues 1645, Estimated correctness of the model 99.6 % 23 chains (1595 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 22 A Built loop between residues 215 A and 218 A Built loop between residues 39 C and 43 C Built loop between residues 75 C and 86 C Built loop between residues 133 C and 137 C Built loop between residues 130 B and 133 B Built loop between residues 18 E and 23 E Built loop between residues 186 E and 196 E Built loop between residues 239 E and 242 E Built loop between residues 37 D and 40 D Built loop between residues 241 D and 244 D Built loop between residues 19 F and 25 F Built loop between residues 72 F and 76 F Built loop between residues 209 F and 212 F 12 chains (1691 residues) following loop building 9 chains (1646 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14220 restraints for refining 14069 atoms. 1003 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1953 (Rfree = 0.000) for 14069 atoms. Found 114 (114 requested) and removed 135 (114 requested) atoms. Cycle 32: After refmac, R = 0.1836 (Rfree = 0.000) for 14031 atoms. Found 113 (113 requested) and removed 114 (113 requested) atoms. Cycle 33: After refmac, R = 0.1768 (Rfree = 0.000) for 14017 atoms. Found 113 (113 requested) and removed 116 (113 requested) atoms. Cycle 34: After refmac, R = 0.1729 (Rfree = 0.000) for 14007 atoms. Found 113 (113 requested) and removed 115 (113 requested) atoms. Cycle 35: After refmac, R = 0.1702 (Rfree = 0.000) for 13996 atoms. Found 113 (113 requested) and removed 116 (113 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.40 2.64 NCS extension: 7 residues added (103 deleted due to clashes), 14005 seeds are put forward Round 1: 1660 peptides, 34 chains. Longest chain 221 peptides. Score 0.960 Round 2: 1663 peptides, 28 chains. Longest chain 198 peptides. Score 0.964 Round 3: 1646 peptides, 46 chains. Longest chain 171 peptides. Score 0.950 Round 4: 1656 peptides, 40 chains. Longest chain 111 peptides. Score 0.955 Round 5: 1643 peptides, 50 chains. Longest chain 145 peptides. Score 0.947 Taking the results from Round 2 Chains 30, Residues 1635, Estimated correctness of the model 99.6 % 26 chains (1600 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 270 A and 273 A Built loop between residues 119 C and 125 C Built loop between residues 139 C and 142 C Built loop between residues 212 C and 215 C Built loop between residues 133 B and 143 B Built loop between residues 191 B and 194 B Built loop between residues 237 B and 240 B Built loop between residues 75 E and 78 E Built loop between residues 133 E and 137 E Built loop between residues 186 E and 190 E Built loop between residues 232 E and 235 E Built loop between residues 66 D and 69 D Built loop between residues 187 D and 190 D Built loop between residues 19 F and 25 F Built loop between residues 280 F and 283 F 13 chains (1677 residues) following loop building 10 chains (1647 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14532 restraints for refining 14101 atoms. 1409 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1936 (Rfree = 0.000) for 14101 atoms. Found 114 (114 requested) and removed 140 (114 requested) atoms. Cycle 37: After refmac, R = 0.1804 (Rfree = 0.000) for 14054 atoms. Found 114 (114 requested) and removed 117 (114 requested) atoms. Cycle 38: After refmac, R = 0.1736 (Rfree = 0.000) for 14046 atoms. Found 113 (113 requested) and removed 113 (113 requested) atoms. Cycle 39: After refmac, R = 0.1699 (Rfree = 0.000) for 14036 atoms. Found 113 (113 requested) and removed 114 (113 requested) atoms. Cycle 40: After refmac, R = 0.1676 (Rfree = 0.000) for 14026 atoms. Found 113 (113 requested) and removed 115 (113 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.39 2.63 NCS extension: 77 residues added (647 deleted due to clashes), 14112 seeds are put forward Round 1: 1666 peptides, 31 chains. Longest chain 218 peptides. Score 0.962 Round 2: 1667 peptides, 30 chains. Longest chain 219 peptides. Score 0.963 Round 3: 1659 peptides, 36 chains. Longest chain 257 peptides. Score 0.958 Round 4: 1651 peptides, 42 chains. Longest chain 99 peptides. Score 0.954 Round 5: 1638 peptides, 49 chains. Longest chain 187 peptides. Score 0.948 Taking the results from Round 2 Chains 32, Residues 1637, Estimated correctness of the model 99.6 % 28 chains (1620 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 77 A Built loop between residues 187 A and 190 A Built loop between residues 265 A and 268 A Built loop between residues 19 C and 23 C Built loop between residues 71 C and 74 C Built loop between residues 133 C and 138 C Built loop between residues 187 C and 190 C Built loop between residues 267 C and 271 C Built loop between residues 31 B and 34 B Built loop between residues 48 B and 52 B Built loop between residues 72 B and 76 B Built loop between residues 184 B and 186 B Built loop between residues 268 B and 275 B Built loop between residues 85 E and 89 E Built loop between residues 133 E and 137 E Built loop between residues 253 E and 256 E Built loop between residues 19 D and 23 D Built loop between residues 72 D and 76 D Built loop between residues 74 F and 85 F Built loop between residues 118 F and 121 F Built loop between residues 212 F and 215 F 9 chains (1700 residues) following loop building 7 chains (1685 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14239 restraints for refining 14152 atoms. 817 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1969 (Rfree = 0.000) for 14152 atoms. Found 114 (114 requested) and removed 140 (114 requested) atoms. Cycle 42: After refmac, R = 0.1841 (Rfree = 0.000) for 14107 atoms. Found 114 (114 requested) and removed 115 (114 requested) atoms. Cycle 43: After refmac, R = 0.1759 (Rfree = 0.000) for 14099 atoms. Found 114 (114 requested) and removed 116 (114 requested) atoms. Cycle 44: After refmac, R = 0.1726 (Rfree = 0.000) for 14094 atoms. Found 114 (114 requested) and removed 117 (114 requested) atoms. Cycle 45: After refmac, R = 0.1710 (Rfree = 0.000) for 14081 atoms. Found 114 (114 requested) and removed 116 (114 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.39 2.63 NCS extension: 29 residues added (56 deleted due to clashes), 14116 seeds are put forward Round 1: 1674 peptides, 34 chains. Longest chain 211 peptides. Score 0.961 Round 2: 1674 peptides, 32 chains. Longest chain 138 peptides. Score 0.962 Round 3: 1652 peptides, 47 chains. Longest chain 107 peptides. Score 0.950 Round 4: 1662 peptides, 43 chains. Longest chain 131 peptides. Score 0.954 Round 5: 1661 peptides, 47 chains. Longest chain 162 peptides. Score 0.951 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 1642, Estimated correctness of the model 99.6 % 29 chains (1613 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 133 A and 137 A Built loop between residues 186 A and 196 A Built loop between residues 19 C and 23 C Built loop between residues 130 C and 133 C Built loop between residues 187 C and 190 C Built loop between residues 267 C and 271 C Built loop between residues 78 B and 83 B Built loop between residues 119 B and 125 B Built loop between residues 139 B and 142 B Built loop between residues 212 B and 216 B Built loop between residues 235 B and 248 B Built loop between residues 30 E and 33 E Built loop between residues 129 E and 132 E Built loop between residues 268 E and 272 E Built loop between residues 72 D and 76 D Built loop between residues 129 D and 132 D Built loop between residues 233 D and 236 D Built loop between residues 270 D and 273 D 15 chains (1698 residues) following loop building 10 chains (1679 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 52578 reflections ( 99.99 % complete ) and 13400 restraints for refining 13226 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2539 (Rfree = 0.000) for 13226 atoms. Found 57 (107 requested) and removed 0 (107 requested) atoms. Cycle 47: After refmac, R = 0.2401 (Rfree = 0.000) for 13226 atoms. Found 34 (107 requested) and removed 10 (107 requested) atoms. Cycle 48: After refmac, R = 0.2339 (Rfree = 0.000) for 13226 atoms. Found 24 (107 requested) and removed 7 (107 requested) atoms. Cycle 49: After refmac, R = 0.2298 (Rfree = 0.000) for 13226 atoms. Found 22 (108 requested) and removed 13 (108 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:48:42 GMT 2018 Job finished. TimeTaking 205.68 Used memory is bytes: 14347224