null Tue 25 Dec 19:27:56 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 1vr5-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-1.7-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/1vr5-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-1.7-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 19:28:11 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/1vr5-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-1.7-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 1464 and 0 Target number of residues in the AU: 1464 Target solvent content: 0.4943 Checking the provided sequence file Detected sequence length: 547 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1094 Adjusted target solvent content: 0.62 Input MTZ file: 1vr5-1.7-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 115.780 1.730 Wilson plot Bfac: 22.33 163658 reflections ( 99.94 % complete ) and 0 restraints for refining 9639 atoms. Observations/parameters ratio is 4.24 ------------------------------------------------------ Starting model: R = 0.3116 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2646 (Rfree = 0.000) for 9639 atoms. Found 499 (499 requested) and removed 168 (249 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.94 1.65 NCS extension: 0 residues added, 9970 seeds are put forward Round 1: 969 peptides, 62 chains. Longest chain 59 peptides. Score 0.795 Round 2: 1031 peptides, 26 chains. Longest chain 247 peptides. Score 0.886 Round 3: 1051 peptides, 15 chains. Longest chain 268 peptides. Score 0.908 Round 4: 1049 peptides, 16 chains. Longest chain 224 peptides. Score 0.906 Round 5: 1047 peptides, 16 chains. Longest chain 263 peptides. Score 0.906 Taking the results from Round 3 Chains 17, Residues 1036, Estimated correctness of the model 99.4 % 14 chains (1023 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A Built loop between residues 114 A and 117 A Built loop between residues 269 A and 279 A Built loop between residues 287 A and 290 A Built loop between residues 428 A and 431 A Built loop between residues 489 A and 494 A Built loop between residues 88 B and 91 B Built loop between residues 154 B and 158 B Built loop between residues 176 B and 179 B Built loop between residues 258 B and 261 B Built loop between residues 276 B and 279 B 4 chains (1062 residues) following loop building 3 chains (1055 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 9817 restraints for refining 9991 atoms. 873 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2535 (Rfree = 0.000) for 9991 atoms. Found 500 (517 requested) and removed 177 (258 requested) atoms. Cycle 2: After refmac, R = 0.2176 (Rfree = 0.000) for 10302 atoms. Found 364 (533 requested) and removed 67 (266 requested) atoms. Cycle 3: After refmac, R = 0.2024 (Rfree = 0.000) for 10544 atoms. Found 342 (548 requested) and removed 82 (274 requested) atoms. Cycle 4: After refmac, R = 0.1926 (Rfree = 0.000) for 10771 atoms. Found 289 (559 requested) and removed 111 (279 requested) atoms. Cycle 5: After refmac, R = 0.1860 (Rfree = 0.000) for 10895 atoms. Found 345 (566 requested) and removed 121 (283 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.90 1.61 NCS extension: 104 residues added (441 deleted due to clashes), 11225 seeds are put forward Round 1: 1057 peptides, 14 chains. Longest chain 205 peptides. Score 0.911 Round 2: 1061 peptides, 8 chains. Longest chain 270 peptides. Score 0.920 Round 3: 1061 peptides, 12 chains. Longest chain 269 peptides. Score 0.915 Round 4: 1060 peptides, 10 chains. Longest chain 270 peptides. Score 0.917 Round 5: 1058 peptides, 12 chains. Longest chain 245 peptides. Score 0.914 Taking the results from Round 2 Chains 12, Residues 1053, Estimated correctness of the model 99.6 % 9 chains (1043 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 166 A and 173 A Built loop between residues 257 A and 261 A Built loop between residues 276 A and 279 A Built loop between residues 372 A and 375 A Built loop between residues 385 A and 388 A Built loop between residues 256 B and 261 B Built loop between residues 275 B and 278 B 3 chains (1068 residues) following loop building 2 chains (1064 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10004 restraints for refining 10375 atoms. 1000 conditional restraints added. Observations/parameters ratio is 3.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1975 (Rfree = 0.000) for 10375 atoms. Found 495 (537 requested) and removed 111 (268 requested) atoms. Cycle 7: After refmac, R = 0.1880 (Rfree = 0.000) for 10736 atoms. Found 309 (556 requested) and removed 159 (278 requested) atoms. Cycle 8: After refmac, R = 0.1819 (Rfree = 0.000) for 10863 atoms. Found 320 (552 requested) and removed 148 (281 requested) atoms. Cycle 9: After refmac, R = 0.1794 (Rfree = 0.000) for 11012 atoms. Found 287 (560 requested) and removed 198 (285 requested) atoms. Cycle 10: After refmac, R = 0.1774 (Rfree = 0.000) for 11074 atoms. Found 337 (551 requested) and removed 189 (287 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 1.61 NCS extension: 0 residues added (4 deleted due to clashes), 11223 seeds are put forward Round 1: 1057 peptides, 15 chains. Longest chain 163 peptides. Score 0.909 Round 2: 1060 peptides, 11 chains. Longest chain 270 peptides. Score 0.916 Round 3: 1056 peptides, 13 chains. Longest chain 248 peptides. Score 0.912 Round 4: 1058 peptides, 12 chains. Longest chain 248 peptides. Score 0.914 Round 5: 1055 peptides, 16 chains. Longest chain 214 peptides. Score 0.908 Taking the results from Round 2 Chains 13, Residues 1049, Estimated correctness of the model 99.5 % 10 chains (1036 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 65 A Built loop between residues 250 A and 261 A Built loop between residues 276 A and 279 A Built loop between residues 442 A and 445 A Built loop between residues 137 B and 140 B Built loop between residues 176 B and 179 B Built loop between residues 256 B and 261 B Built loop between residues 275 B and 278 B 3 chains (1068 residues) following loop building 2 chains (1064 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10119 restraints for refining 10495 atoms. 1111 conditional restraints added. Observations/parameters ratio is 3.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1923 (Rfree = 0.000) for 10495 atoms. Found 478 (510 requested) and removed 113 (271 requested) atoms. Cycle 12: After refmac, R = 0.1852 (Rfree = 0.000) for 10841 atoms. Found 311 (528 requested) and removed 152 (281 requested) atoms. Cycle 13: After refmac, R = 0.1814 (Rfree = 0.000) for 10981 atoms. Found 324 (535 requested) and removed 134 (284 requested) atoms. Cycle 14: After refmac, R = 0.1784 (Rfree = 0.000) for 11157 atoms. Found 288 (543 requested) and removed 191 (289 requested) atoms. Cycle 15: After refmac, R = 0.1779 (Rfree = 0.000) for 11225 atoms. Found 343 (535 requested) and removed 183 (291 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 1.61 NCS extension: 0 residues added (3 deleted due to clashes), 11389 seeds are put forward Round 1: 1056 peptides, 16 chains. Longest chain 163 peptides. Score 0.908 Round 2: 1060 peptides, 13 chains. Longest chain 206 peptides. Score 0.913 Round 3: 1060 peptides, 12 chains. Longest chain 250 peptides. Score 0.914 Round 4: 1056 peptides, 11 chains. Longest chain 215 peptides. Score 0.915 Round 5: 1051 peptides, 17 chains. Longest chain 178 peptides. Score 0.905 Taking the results from Round 4 Chains 11, Residues 1045, Estimated correctness of the model 99.5 % 10 chains (1039 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 204 A and 207 A Built loop between residues 250 A and 261 A Built loop between residues 277 A and 283 A Built loop between residues 439 A and 443 A Built loop between residues 177 B and 180 B Built loop between residues 276 B and 279 B Built loop between residues 492 B and 495 B Built loop between residues 520 B and 523 B 2 chains (1067 residues) following loop building 2 chains (1067 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10145 restraints for refining 10597 atoms. 1124 conditional restraints added. Observations/parameters ratio is 3.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1941 (Rfree = 0.000) for 10597 atoms. Found 479 (493 requested) and removed 121 (274 requested) atoms. Cycle 17: After refmac, R = 0.1851 (Rfree = 0.000) for 10927 atoms. Found 362 (510 requested) and removed 157 (283 requested) atoms. Cycle 18: After refmac, R = 0.1807 (Rfree = 0.000) for 11112 atoms. Found 296 (518 requested) and removed 162 (288 requested) atoms. Cycle 19: After refmac, R = 0.1779 (Rfree = 0.000) for 11228 atoms. Found 276 (512 requested) and removed 171 (291 requested) atoms. Cycle 20: After refmac, R = 0.1755 (Rfree = 0.000) for 11307 atoms. Found 281 (504 requested) and removed 169 (293 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 1.61 NCS extension: 0 residues added, 11420 seeds are put forward Round 1: 1051 peptides, 15 chains. Longest chain 164 peptides. Score 0.908 Round 2: 1060 peptides, 8 chains. Longest chain 270 peptides. Score 0.920 Round 3: 1059 peptides, 12 chains. Longest chain 248 peptides. Score 0.914 Round 4: 1051 peptides, 13 chains. Longest chain 256 peptides. Score 0.911 Round 5: 1056 peptides, 14 chains. Longest chain 214 peptides. Score 0.911 Taking the results from Round 2 Chains 8, Residues 1052, Estimated correctness of the model 99.6 % 8 chains (1052 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 141 A Built loop between residues 256 A and 261 A Built loop between residues 276 A and 279 A Built loop between residues 439 A and 442 A Built loop between residues 259 B and 262 B Built loop between residues 275 B and 278 B 2 chains (1067 residues) following loop building 2 chains (1067 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10192 restraints for refining 10628 atoms. 1175 conditional restraints added. Observations/parameters ratio is 3.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1913 (Rfree = 0.000) for 10628 atoms. Found 462 (462 requested) and removed 114 (275 requested) atoms. Cycle 22: After refmac, R = 0.1831 (Rfree = 0.000) for 10949 atoms. Found 326 (477 requested) and removed 130 (284 requested) atoms. Cycle 23: After refmac, R = 0.1793 (Rfree = 0.000) for 11124 atoms. Found 294 (484 requested) and removed 122 (288 requested) atoms. Cycle 24: After refmac, R = 0.1760 (Rfree = 0.000) for 11280 atoms. Found 252 (491 requested) and removed 170 (292 requested) atoms. Cycle 25: After refmac, R = 0.1748 (Rfree = 0.000) for 11334 atoms. Found 308 (482 requested) and removed 181 (294 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.90 1.61 NCS extension: 0 residues added, 11462 seeds are put forward Round 1: 1059 peptides, 13 chains. Longest chain 214 peptides. Score 0.913 Round 2: 1060 peptides, 9 chains. Longest chain 246 peptides. Score 0.919 Round 3: 1060 peptides, 11 chains. Longest chain 270 peptides. Score 0.916 Round 4: 1055 peptides, 10 chains. Longest chain 266 peptides. Score 0.916 Round 5: 1056 peptides, 15 chains. Longest chain 160 peptides. Score 0.909 Taking the results from Round 2 Chains 9, Residues 1051, Estimated correctness of the model 99.6 % 9 chains (1051 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 168 A Built loop between residues 256 A and 261 A Built loop between residues 275 A and 278 A Built loop between residues 384 A and 387 A Built loop between residues 257 B and 260 B Built loop between residues 275 B and 278 B Built loop between residues 339 B and 342 B 2 chains (1067 residues) following loop building 2 chains (1067 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10209 restraints for refining 10669 atoms. 1188 conditional restraints added. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1902 (Rfree = 0.000) for 10669 atoms. Found 442 (442 requested) and removed 109 (276 requested) atoms. Cycle 27: After refmac, R = 0.1822 (Rfree = 0.000) for 10966 atoms. Found 304 (455 requested) and removed 165 (284 requested) atoms. Cycle 28: After refmac, R = 0.1776 (Rfree = 0.000) for 11081 atoms. Found 338 (448 requested) and removed 133 (287 requested) atoms. Cycle 29: After refmac, R = 0.1753 (Rfree = 0.000) for 11268 atoms. Found 277 (456 requested) and removed 171 (292 requested) atoms. Cycle 30: After refmac, R = 0.1744 (Rfree = 0.000) for 11337 atoms. Found 327 (447 requested) and removed 171 (294 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.90 1.61 NCS extension: 0 residues added, 11493 seeds are put forward Round 1: 1056 peptides, 15 chains. Longest chain 213 peptides. Score 0.909 Round 2: 1058 peptides, 11 chains. Longest chain 216 peptides. Score 0.915 Round 3: 1058 peptides, 13 chains. Longest chain 248 peptides. Score 0.913 Round 4: 1062 peptides, 10 chains. Longest chain 248 peptides. Score 0.918 Round 5: 1054 peptides, 16 chains. Longest chain 213 peptides. Score 0.907 Taking the results from Round 4 Chains 12, Residues 1052, Estimated correctness of the model 99.5 % 9 chains (1040 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A Built loop between residues 258 A and 261 A Built loop between residues 268 A and 278 A Built loop between residues 492 A and 495 A Built loop between residues 256 B and 262 B Built loop between residues 276 B and 279 B Built loop between residues 337 B and 340 B 3 chains (1068 residues) following loop building 2 chains (1064 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10280 restraints for refining 10683 atoms. 1276 conditional restraints added. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1904 (Rfree = 0.000) for 10683 atoms. Found 409 (409 requested) and removed 112 (276 requested) atoms. Cycle 32: After refmac, R = 0.1819 (Rfree = 0.000) for 10948 atoms. Found 332 (420 requested) and removed 122 (284 requested) atoms. Cycle 33: After refmac, R = 0.1779 (Rfree = 0.000) for 11136 atoms. Found 330 (427 requested) and removed 139 (288 requested) atoms. Cycle 34: After refmac, R = 0.1758 (Rfree = 0.000) for 11300 atoms. Found 272 (434 requested) and removed 178 (293 requested) atoms. Cycle 35: After refmac, R = 0.1751 (Rfree = 0.000) for 11364 atoms. Found 316 (424 requested) and removed 155 (294 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.90 1.61 NCS extension: 0 residues added (4 deleted due to clashes), 11525 seeds are put forward Round 1: 1059 peptides, 12 chains. Longest chain 163 peptides. Score 0.914 Round 2: 1056 peptides, 11 chains. Longest chain 245 peptides. Score 0.915 Round 3: 1060 peptides, 11 chains. Longest chain 248 peptides. Score 0.916 Round 4: 1058 peptides, 11 chains. Longest chain 248 peptides. Score 0.915 Round 5: 1057 peptides, 13 chains. Longest chain 248 peptides. Score 0.912 Taking the results from Round 3 Chains 11, Residues 1049, Estimated correctness of the model 99.5 % 9 chains (1036 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 47 A Built loop between residues 165 A and 168 A Built loop between residues 259 A and 262 A Built loop between residues 275 A and 278 A Built loop between residues 440 A and 443 A Built loop between residues 453 B and 456 B 5 chains (1061 residues) following loop building 3 chains (1048 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10511 restraints for refining 10708 atoms. 1597 conditional restraints added. Observations/parameters ratio is 3.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1916 (Rfree = 0.000) for 10708 atoms. Found 399 (399 requested) and removed 113 (277 requested) atoms. Cycle 37: After refmac, R = 0.1834 (Rfree = 0.000) for 10964 atoms. Found 328 (410 requested) and removed 113 (284 requested) atoms. Cycle 38: After refmac, R = 0.1796 (Rfree = 0.000) for 11156 atoms. Found 305 (416 requested) and removed 146 (289 requested) atoms. Cycle 39: After refmac, R = 0.1765 (Rfree = 0.000) for 11300 atoms. Found 268 (421 requested) and removed 157 (292 requested) atoms. Cycle 40: After refmac, R = 0.1753 (Rfree = 0.000) for 11380 atoms. Found 310 (413 requested) and removed 184 (295 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.90 1.61 NCS extension: 152 residues added (400 deleted due to clashes), 11658 seeds are put forward Round 1: 1060 peptides, 14 chains. Longest chain 177 peptides. Score 0.912 Round 2: 1058 peptides, 10 chains. Longest chain 270 peptides. Score 0.917 Round 3: 1059 peptides, 10 chains. Longest chain 270 peptides. Score 0.917 Round 4: 1063 peptides, 9 chains. Longest chain 270 peptides. Score 0.919 Round 5: 1060 peptides, 12 chains. Longest chain 215 peptides. Score 0.914 Taking the results from Round 4 Chains 9, Residues 1054, Estimated correctness of the model 99.6 % 9 chains (1054 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 275 A and 278 A Built loop between residues 339 A and 342 A Built loop between residues 518 A and 521 A Built loop between residues 137 B and 140 B Built loop between residues 275 B and 278 B 4 chains (1064 residues) following loop building 4 chains (1064 residues) in sequence following loop building ------------------------------------------------------ 163658 reflections ( 99.94 % complete ) and 10323 restraints for refining 10706 atoms. 1341 conditional restraints added. Observations/parameters ratio is 3.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1898 (Rfree = 0.000) for 10706 atoms. Found 377 (377 requested) and removed 120 (277 requested) atoms. Cycle 42: After refmac, R = 0.1825 (Rfree = 0.000) for 10943 atoms. Found 332 (386 requested) and removed 123 (283 requested) atoms. Cycle 43: After refmac, R = 0.1789 (Rfree = 0.000) for 11134 atoms. Found 320 (392 requested) and removed 172 (288 requested) atoms. Cycle 44: After refmac, R = 0.1765 (Rfree = 0.000) for 11254 atoms. Found 329 (385 requested) and removed 186 (291 requested) atoms. Cycle 45: After refmac, R = 0.1754 (Rfree = 0.000) for 11380 atoms. Found 317 (377 requested) and removed 203 (294 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.90 1.61 NCS extension: 0 residues added, 11495 seeds are put forward Round 1: 1061 peptides, 11 chains. Longest chain 270 peptides. Score 0.916 Round 2: 1059 peptides, 10 chains. Longest chain 265 peptides. Score 0.917 Round 3: 1054 peptides, 13 chains. Longest chain 214 peptides. Score 0.912 Round 4: 1060 peptides, 8 chains. Longest chain 269 peptides. Score 0.920 Round 5: 1056 peptides, 13 chains. Longest chain 214 peptides. Score 0.912 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 1052, Estimated correctness of the model 99.6 % 7 chains (1045 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 256 A and 261 A Built loop between residues 268 A and 278 A Built loop between residues 257 B and 262 B Built loop between residues 276 B and 279 B Built loop between residues 387 B and 390 B 2 chains (1066 residues) following loop building 2 chains (1066 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 163658 reflections ( 99.94 % complete ) and 9012 restraints for refining 8714 atoms. Observations/parameters ratio is 4.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2403 (Rfree = 0.000) for 8714 atoms. Found 280 (280 requested) and removed 0 (280 requested) atoms. Cycle 47: After refmac, R = 0.2174 (Rfree = 0.000) for 8714 atoms. Found 217 (288 requested) and removed 0 (232 requested) atoms. Cycle 48: After refmac, R = 0.2000 (Rfree = 0.000) for 8714 atoms. Found 77 (295 requested) and removed 4 (238 requested) atoms. Cycle 49: After refmac, R = 0.1916 (Rfree = 0.000) for 8714 atoms. Found 60 (298 requested) and removed 12 (240 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 23:09:00 GMT 2018 Job finished. TimeTaking 221.07 Used memory is bytes: 20779816