null Mon 24 Dec 08:08:13 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2obn-2.3-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2obn-2.3-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2obn-2.3-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 08:08:17 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1172 and 0 Target number of residues in the AU: 1172 Target solvent content: 0.5306 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-2.3-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-2.3-parrot-noncs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.45 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: 73.214 2.300 Wilson plot Bfac: 30.44 58827 reflections ( 99.75 % complete ) and 0 restraints for refining 12303 atoms. Observations/parameters ratio is 1.20 ------------------------------------------------------ Starting model: R = 0.3129 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2200 (Rfree = 0.000) for 12303 atoms. Found 181 (282 requested) and removed 165 (141 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.34 2.54 NCS extension: 0 residues added, 12319 seeds are put forward Round 1: 765 peptides, 132 chains. Longest chain 17 peptides. Score 0.458 Round 2: 914 peptides, 103 chains. Longest chain 36 peptides. Score 0.700 Round 3: 989 peptides, 98 chains. Longest chain 33 peptides. Score 0.760 Round 4: 1021 peptides, 81 chains. Longest chain 63 peptides. Score 0.816 Round 5: 1054 peptides, 77 chains. Longest chain 50 peptides. Score 0.838 Taking the results from Round 5 Chains 90, Residues 977, Estimated correctness of the model 96.0 % 33 chains (623 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 181 A and 185 A Built loop between residues 248 A and 253 A Built loop between residues 279 A and 282 A Built loop between residues 193 C and 200 C Built loop between residues 213 C and 216 C Built loop between residues 252 C and 256 C Built loop between residues 164 B and 167 B Built loop between residues 197 B and 202 B Built loop between residues 218 B and 221 B Built loop between residues 239 B and 244 B Built loop between residues 270 B and 280 B 78 chains (1017 residues) following loop building 22 chains (664 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 15508 restraints for refining 10583 atoms. 9176 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2702 (Rfree = 0.000) for 10583 atoms. Found 228 (243 requested) and removed 134 (121 requested) atoms. Cycle 2: After refmac, R = 0.2474 (Rfree = 0.000) for 10552 atoms. Found 156 (240 requested) and removed 126 (122 requested) atoms. Cycle 3: After refmac, R = 0.2248 (Rfree = 0.000) for 10500 atoms. Found 122 (233 requested) and removed 121 (121 requested) atoms. Cycle 4: After refmac, R = 0.2149 (Rfree = 0.000) for 10452 atoms. Found 77 (227 requested) and removed 111 (120 requested) atoms. Cycle 5: After refmac, R = 0.2107 (Rfree = 0.000) for 10393 atoms. Found 86 (220 requested) and removed 63 (119 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.30 2.49 NCS extension: 221 residues added (769 deleted due to clashes), 10681 seeds are put forward Round 1: 1061 peptides, 57 chains. Longest chain 125 peptides. Score 0.876 Round 2: 1097 peptides, 45 chains. Longest chain 104 peptides. Score 0.904 Round 3: 1108 peptides, 49 chains. Longest chain 168 peptides. Score 0.901 Round 4: 1112 peptides, 45 chains. Longest chain 108 peptides. Score 0.908 Round 5: 1088 peptides, 51 chains. Longest chain 144 peptides. Score 0.893 Taking the results from Round 4 Chains 51, Residues 1067, Estimated correctness of the model 98.6 % 25 chains (886 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 168 A and 171 A Built loop between residues 276 A and 282 A Built loop between residues 65 C and 69 C Built loop between residues 236 C and 239 C Built loop between residues 251 C and 254 C Built loop between residues 290 C and 295 C Built loop between residues 35 B and 46 B Built loop between residues 219 B and 223 B Built loop between residues 243 B and 252 B Built loop between residues 163 D and 166 D Built loop between residues 206 D and 209 D Built loop between residues 253 D and 255 D Built loop between residues 274 D and 278 D 36 chains (1108 residues) following loop building 12 chains (933 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 13089 restraints for refining 10590 atoms. 5336 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2343 (Rfree = 0.000) for 10590 atoms. Found 170 (219 requested) and removed 152 (121 requested) atoms. Cycle 7: After refmac, R = 0.2154 (Rfree = 0.000) for 10565 atoms. Found 122 (215 requested) and removed 122 (122 requested) atoms. Cycle 8: After refmac, R = 0.2071 (Rfree = 0.000) for 10540 atoms. Found 114 (209 requested) and removed 119 (121 requested) atoms. Cycle 9: After refmac, R = 0.2008 (Rfree = 0.000) for 10513 atoms. Found 73 (203 requested) and removed 56 (121 requested) atoms. Cycle 10: After refmac, R = 0.1979 (Rfree = 0.000) for 10511 atoms. Found 62 (198 requested) and removed 44 (121 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.31 2.50 NCS extension: 322 residues added (505 deleted due to clashes), 10874 seeds are put forward Round 1: 1132 peptides, 48 chains. Longest chain 134 peptides. Score 0.908 Round 2: 1170 peptides, 39 chains. Longest chain 140 peptides. Score 0.927 Round 3: 1164 peptides, 49 chains. Longest chain 92 peptides. Score 0.913 Round 4: 1160 peptides, 41 chains. Longest chain 98 peptides. Score 0.923 Round 5: 1117 peptides, 53 chains. Longest chain 124 peptides. Score 0.897 Taking the results from Round 2 Chains 44, Residues 1131, Estimated correctness of the model 99.1 % 20 chains (973 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 173 A and 177 A Built loop between residues 316 A and 319 A Built loop between residues 218 C and 221 C Built loop between residues 26 B and 29 B Built loop between residues 222 B and 225 B Built loop between residues 270 B and 273 B Built loop between residues 327 B and 330 B Built loop between residues 197 D and 201 D Built loop between residues 240 D and 243 D 34 chains (1150 residues) following loop building 11 chains (993 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 12380 restraints for refining 10590 atoms. 4232 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2133 (Rfree = 0.000) for 10590 atoms. Found 175 (194 requested) and removed 132 (121 requested) atoms. Cycle 12: After refmac, R = 0.2008 (Rfree = 0.000) for 10611 atoms. Found 90 (190 requested) and removed 122 (122 requested) atoms. Cycle 13: After refmac, R = 0.1960 (Rfree = 0.000) for 10558 atoms. Found 84 (185 requested) and removed 85 (121 requested) atoms. Cycle 14: After refmac, R = 0.1929 (Rfree = 0.000) for 10540 atoms. Found 86 (179 requested) and removed 57 (121 requested) atoms. Cycle 15: After refmac, R = 0.1899 (Rfree = 0.000) for 10561 atoms. Found 72 (175 requested) and removed 62 (121 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.31 2.50 NCS extension: 577 residues added (668 deleted due to clashes), 11157 seeds are put forward Round 1: 1155 peptides, 43 chains. Longest chain 135 peptides. Score 0.919 Round 2: 1186 peptides, 37 chains. Longest chain 152 peptides. Score 0.932 Round 3: 1184 peptides, 41 chains. Longest chain 129 peptides. Score 0.927 Round 4: 1170 peptides, 40 chains. Longest chain 205 peptides. Score 0.926 Round 5: 1173 peptides, 47 chains. Longest chain 169 peptides. Score 0.918 Taking the results from Round 2 Chains 42, Residues 1149, Estimated correctness of the model 99.2 % 24 chains (1049 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 172 A and 176 A Built loop between residues 251 A and 255 A Built loop between residues 49 C and 57 C Built loop between residues 82 C and 92 C Built loop between residues 144 C and 147 C Built loop between residues 194 C and 197 C Built loop between residues 247 C and 251 C Built loop between residues 304 C and 314 C Built loop between residues 28 B and 31 B Built loop between residues 45 B and 48 B Built loop between residues 117 B and 120 B Built loop between residues 143 B and 146 B Built loop between residues 296 B and 302 B Built loop between residues 252 D and 255 D 27 chains (1200 residues) following loop building 10 chains (1102 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11783 restraints for refining 10697 atoms. 3033 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2088 (Rfree = 0.000) for 10697 atoms. Found 172 (172 requested) and removed 130 (123 requested) atoms. Cycle 17: After refmac, R = 0.1941 (Rfree = 0.000) for 10720 atoms. Found 114 (168 requested) and removed 123 (123 requested) atoms. Cycle 18: After refmac, R = 0.1879 (Rfree = 0.000) for 10697 atoms. Found 84 (162 requested) and removed 123 (123 requested) atoms. Cycle 19: After refmac, R = 0.1857 (Rfree = 0.000) for 10649 atoms. Found 94 (157 requested) and removed 72 (122 requested) atoms. Cycle 20: After refmac, R = 0.1826 (Rfree = 0.000) for 10653 atoms. Found 82 (152 requested) and removed 78 (122 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.30 2.49 NCS extension: 499 residues added (613 deleted due to clashes), 11171 seeds are put forward Round 1: 1200 peptides, 46 chains. Longest chain 106 peptides. Score 0.924 Round 2: 1219 peptides, 33 chains. Longest chain 220 peptides. Score 0.941 Round 3: 1204 peptides, 45 chains. Longest chain 159 peptides. Score 0.926 Round 4: 1216 peptides, 37 chains. Longest chain 194 peptides. Score 0.937 Round 5: 1202 peptides, 43 chains. Longest chain 96 peptides. Score 0.928 Taking the results from Round 2 Chains 34, Residues 1186, Estimated correctness of the model 99.4 % 15 chains (1056 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 194 A and 197 A Built loop between residues 24 B and 27 B Built loop between residues 296 B and 301 B Built loop between residues 163 D and 166 D 29 chains (1194 residues) following loop building 11 chains (1066 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 12006 restraints for refining 10590 atoms. 3419 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2009 (Rfree = 0.000) for 10590 atoms. Found 146 (146 requested) and removed 128 (121 requested) atoms. Cycle 22: After refmac, R = 0.1882 (Rfree = 0.000) for 10593 atoms. Found 126 (142 requested) and removed 122 (122 requested) atoms. Cycle 23: After refmac, R = 0.1827 (Rfree = 0.000) for 10588 atoms. Found 107 (136 requested) and removed 68 (121 requested) atoms. Cycle 24: After refmac, R = 0.1797 (Rfree = 0.000) for 10619 atoms. Found 89 (132 requested) and removed 68 (122 requested) atoms. Cycle 25: After refmac, R = 0.1767 (Rfree = 0.000) for 10636 atoms. Found 105 (127 requested) and removed 71 (122 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.30 2.49 NCS extension: 283 residues added (846 deleted due to clashes), 10961 seeds are put forward Round 1: 1221 peptides, 42 chains. Longest chain 163 peptides. Score 0.932 Round 2: 1233 peptides, 33 chains. Longest chain 198 peptides. Score 0.943 Round 3: 1228 peptides, 43 chains. Longest chain 162 peptides. Score 0.932 Round 4: 1225 peptides, 38 chains. Longest chain 141 peptides. Score 0.937 Round 5: 1217 peptides, 40 chains. Longest chain 129 peptides. Score 0.933 Taking the results from Round 2 Chains 37, Residues 1200, Estimated correctness of the model 99.4 % 18 chains (1041 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 166 A Built loop between residues 252 A and 255 A Built loop between residues 243 C and 246 C Built loop between residues 318 C and 323 C Built loop between residues 50 B and 57 B Built loop between residues 326 B and 331 B Built loop between residues 163 D and 166 D Built loop between residues 271 D and 274 D 28 chains (1222 residues) following loop building 10 chains (1065 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 12126 restraints for refining 10660 atoms. 3408 conditional restraints added. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1979 (Rfree = 0.000) for 10660 atoms. Found 122 (122 requested) and removed 135 (122 requested) atoms. Cycle 27: After refmac, R = 0.1851 (Rfree = 0.000) for 10635 atoms. Found 122 (122 requested) and removed 122 (122 requested) atoms. Cycle 28: After refmac, R = 0.1792 (Rfree = 0.000) for 10629 atoms. Found 119 (122 requested) and removed 76 (122 requested) atoms. Cycle 29: After refmac, R = 0.1756 (Rfree = 0.000) for 10667 atoms. Found 92 (122 requested) and removed 68 (122 requested) atoms. Cycle 30: After refmac, R = 0.1737 (Rfree = 0.000) for 10680 atoms. Found 116 (122 requested) and removed 66 (122 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.30 2.49 NCS extension: 432 residues added (1165 deleted due to clashes), 11171 seeds are put forward Round 1: 1226 peptides, 37 chains. Longest chain 183 peptides. Score 0.938 Round 2: 1240 peptides, 29 chains. Longest chain 237 peptides. Score 0.948 Round 3: 1248 peptides, 36 chains. Longest chain 148 peptides. Score 0.942 Round 4: 1243 peptides, 43 chains. Longest chain 110 peptides. Score 0.934 Round 5: 1211 peptides, 43 chains. Longest chain 134 peptides. Score 0.929 Taking the results from Round 2 Chains 35, Residues 1211, Estimated correctness of the model 99.5 % 15 chains (1088 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 217 B and 220 B Built loop between residues 50 D and 59 D Built loop between residues 83 D and 88 D Built loop between residues 122 D and 125 D 31 chains (1227 residues) following loop building 11 chains (1104 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11876 restraints for refining 10706 atoms. 3000 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1927 (Rfree = 0.000) for 10706 atoms. Found 123 (123 requested) and removed 127 (123 requested) atoms. Cycle 32: After refmac, R = 0.1817 (Rfree = 0.000) for 10692 atoms. Found 123 (123 requested) and removed 123 (123 requested) atoms. Cycle 33: After refmac, R = 0.1769 (Rfree = 0.000) for 10686 atoms. Found 112 (122 requested) and removed 104 (122 requested) atoms. Cycle 34: After refmac, R = 0.1742 (Rfree = 0.000) for 10691 atoms. Found 102 (122 requested) and removed 90 (122 requested) atoms. Cycle 35: After refmac, R = 0.1731 (Rfree = 0.000) for 10689 atoms. Found 109 (123 requested) and removed 77 (123 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.30 2.49 NCS extension: 446 residues added (953 deleted due to clashes), 11179 seeds are put forward Round 1: 1229 peptides, 40 chains. Longest chain 178 peptides. Score 0.935 Round 2: 1248 peptides, 30 chains. Longest chain 221 peptides. Score 0.948 Round 3: 1242 peptides, 35 chains. Longest chain 197 peptides. Score 0.942 Round 4: 1236 peptides, 38 chains. Longest chain 107 peptides. Score 0.938 Round 5: 1227 peptides, 41 chains. Longest chain 158 peptides. Score 0.934 Taking the results from Round 2 Chains 34, Residues 1218, Estimated correctness of the model 99.5 % 17 chains (1126 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 271 A and 274 A Built loop between residues 253 B and 256 B Built loop between residues 326 B and 332 B Built loop between residues 306 D and 314 D 28 chains (1235 residues) following loop building 12 chains (1144 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11616 restraints for refining 10737 atoms. 2576 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1928 (Rfree = 0.000) for 10737 atoms. Found 123 (123 requested) and removed 135 (123 requested) atoms. Cycle 37: After refmac, R = 0.1821 (Rfree = 0.000) for 10709 atoms. Found 123 (123 requested) and removed 123 (123 requested) atoms. Cycle 38: After refmac, R = 0.1773 (Rfree = 0.000) for 10700 atoms. Found 115 (123 requested) and removed 79 (123 requested) atoms. Cycle 39: After refmac, R = 0.1741 (Rfree = 0.000) for 10732 atoms. Found 118 (123 requested) and removed 86 (123 requested) atoms. Cycle 40: After refmac, R = 0.1724 (Rfree = 0.000) for 10756 atoms. Found 121 (123 requested) and removed 96 (123 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.30 2.49 NCS extension: 597 residues added (782 deleted due to clashes), 11387 seeds are put forward Round 1: 1242 peptides, 31 chains. Longest chain 130 peptides. Score 0.946 Round 2: 1257 peptides, 28 chains. Longest chain 211 peptides. Score 0.951 Round 3: 1234 peptides, 35 chains. Longest chain 150 peptides. Score 0.941 Round 4: 1233 peptides, 43 chains. Longest chain 109 peptides. Score 0.933 Round 5: 1226 peptides, 42 chains. Longest chain 176 peptides. Score 0.933 Taking the results from Round 2 Chains 34, Residues 1229, Estimated correctness of the model 99.6 % 18 chains (1117 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 57 A Built loop between residues 304 A and 314 A Built loop between residues 144 C and 147 C Built loop between residues 243 B and 246 B Built loop between residues 281 B and 284 B Built loop between residues 327 B and 331 B Built loop between residues 81 D and 89 D 25 chains (1257 residues) following loop building 11 chains (1149 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11655 restraints for refining 10784 atoms. 2534 conditional restraints added. Observations/parameters ratio is 1.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1930 (Rfree = 0.000) for 10784 atoms. Found 124 (124 requested) and removed 130 (124 requested) atoms. Cycle 42: After refmac, R = 0.1813 (Rfree = 0.000) for 10769 atoms. Found 123 (123 requested) and removed 123 (123 requested) atoms. Cycle 43: After refmac, R = 0.1755 (Rfree = 0.000) for 10768 atoms. Found 117 (123 requested) and removed 101 (123 requested) atoms. Cycle 44: After refmac, R = 0.1738 (Rfree = 0.000) for 10780 atoms. Found 116 (124 requested) and removed 119 (124 requested) atoms. Cycle 45: After refmac, R = 0.1733 (Rfree = 0.000) for 10770 atoms. Found 119 (123 requested) and removed 88 (123 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.30 2.49 NCS extension: 170 residues added (1155 deleted due to clashes), 10981 seeds are put forward Round 1: 1230 peptides, 33 chains. Longest chain 126 peptides. Score 0.943 Round 2: 1245 peptides, 29 chains. Longest chain 222 peptides. Score 0.949 Round 3: 1235 peptides, 37 chains. Longest chain 126 peptides. Score 0.939 Round 4: 1239 peptides, 34 chains. Longest chain 110 peptides. Score 0.943 Round 5: 1233 peptides, 38 chains. Longest chain 128 peptides. Score 0.938 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 1216, Estimated correctness of the model 99.5 % 21 chains (1145 residues) have been docked in sequence Sequence coverage is 94 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 164 A and 167 A Built loop between residues 215 A and 218 A Built loop between residues 270 A and 273 A Built loop between residues 82 C and 95 C Built loop between residues 50 B and 58 B Built loop between residues 84 B and 88 B Built loop between residues 196 B and 199 B Built loop between residues 271 B and 274 B Built loop between residues 307 B and 317 B Built loop between residues 83 D and 91 D Built loop between residues 118 D and 130 D Built loop between residues 196 D and 202 D Built loop between residues 282 D and 285 D 16 chains (1279 residues) following loop building 8 chains (1211 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 58827 reflections ( 99.75 % complete ) and 9475 restraints for refining 9305 atoms. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2664 (Rfree = 0.000) for 9305 atoms. Found 81 (107 requested) and removed 0 (107 requested) atoms. Cycle 47: After refmac, R = 0.2480 (Rfree = 0.000) for 9305 atoms. Found 33 (107 requested) and removed 3 (107 requested) atoms. Cycle 48: After refmac, R = 0.2412 (Rfree = 0.000) for 9305 atoms. Found 19 (108 requested) and removed 10 (108 requested) atoms. Cycle 49: After refmac, R = 0.2387 (Rfree = 0.000) for 9305 atoms. Found 13 (108 requested) and removed 7 (108 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:20:11 GMT 2018 Job finished. TimeTaking 131.97 Used memory is bytes: 5467600