Starting phenix.real_space_refine on Thu Mar 5 01:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qo6_53258/03_2026/9qo6_53258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qo6_53258/03_2026/9qo6_53258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qo6_53258/03_2026/9qo6_53258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qo6_53258/03_2026/9qo6_53258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qo6_53258/03_2026/9qo6_53258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qo6_53258/03_2026/9qo6_53258.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 102 5.16 5 C 11045 2.51 5 N 2962 2.21 5 O 3270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17380 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2352 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 1 Chain: "A" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 2 Chain: "B" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1097 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "C" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3234 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 13, 'TRANS': 393} Chain: "D" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2143 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 260} Chain: "F" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2216 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1694 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1367 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 161} Chain breaks: 1 Chain: "P" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 3.48, per 1000 atoms: 0.20 Number of scatterers: 17380 At special positions: 0 Unit cell: (123.12, 142.56, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 102 16.00 O 3270 8.00 N 2962 7.00 C 11045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 740.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 140 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 138 " 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 6 sheets defined 68.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.987A pdb=" N ASP E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS E 49 " --> pdb=" O TRP E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 44 through 49' Processing helix chain 'E' and resid 59 through 72 removed outlier: 3.790A pdb=" N GLY E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 125 removed outlier: 3.898A pdb=" N ALA E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 125 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.754A pdb=" N GLN E 160 " --> pdb=" O MET E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.612A pdb=" N VAL E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.709A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 281 removed outlier: 3.645A pdb=" N ALA E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN E 279 " --> pdb=" O GLN E 275 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 329 removed outlier: 3.604A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.779A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.328A pdb=" N LYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.515A pdb=" N GLU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 156 removed outlier: 3.690A pdb=" N ASP A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 removed outlier: 4.020A pdb=" N GLY A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.697A pdb=" N LYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.636A pdb=" N VAL A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.507A pdb=" N SER A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.518A pdb=" N LEU A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.534A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 4.185A pdb=" N ALA A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.656A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.857A pdb=" N THR A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.668A pdb=" N ASP A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 463 removed outlier: 4.373A pdb=" N ALA A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.673A pdb=" N ASP B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 363 removed outlier: 5.389A pdb=" N GLU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 350 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 441 removed outlier: 3.671A pdb=" N LYS B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.512A pdb=" N SER C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.622A pdb=" N VAL C 45 " --> pdb=" O HIS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 3.734A pdb=" N ALA C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.939A pdb=" N LEU C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.717A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 94' Processing helix chain 'C' and resid 98 through 115 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 130 removed outlier: 4.647A pdb=" N ILE C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.746A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.742A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.604A pdb=" N HIS C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.537A pdb=" N PHE C 286 " --> pdb=" O HIS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.661A pdb=" N CYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 329 through 345 removed outlier: 4.402A pdb=" N GLU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 399 removed outlier: 3.886A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.552A pdb=" N GLY C 409 " --> pdb=" O GLN C 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 160 through 172 removed outlier: 3.651A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 removed outlier: 3.711A pdb=" N GLN D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.949A pdb=" N ALA D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.603A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.575A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.501A pdb=" N LEU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 365 through 392 Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'F' and resid 44 through 63 removed outlier: 4.127A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 116 removed outlier: 3.773A pdb=" N TYR F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 115 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.543A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 216 through 248 removed outlier: 4.454A pdb=" N ILE F 222 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 272 through 313 removed outlier: 3.975A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 removed outlier: 3.506A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.605A pdb=" N LEU G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.506A pdb=" N GLU G 48 " --> pdb=" O GLU G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 60 through 73 removed outlier: 3.749A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 106 removed outlier: 3.820A pdb=" N ASN G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.692A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 222 removed outlier: 3.825A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 removed outlier: 3.550A pdb=" N GLU H 24 " --> pdb=" O CYS H 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.528A pdb=" N VAL H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.751A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.548A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 152 removed outlier: 3.735A pdb=" N GLY H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 209 Processing sheet with id=AA1, first strand: chain 'E' and resid 54 through 58 removed outlier: 6.817A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N PHE E 96 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP E 86 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE E 92 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS E 84 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP E 94 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY E 135 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 229 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 349 through 352 removed outlier: 5.805A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN D 317 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'F' and resid 178 through 185 removed outlier: 3.617A pdb=" N PHE F 151 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N LEU F 150 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU F 122 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU F 152 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'H' and resid 128 through 129 removed outlier: 3.977A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 3069 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5718 1.34 - 1.46: 3472 1.46 - 1.58: 8336 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 17690 Sorted by residual: bond pdb=" N ASP P 55 " pdb=" CA ASP P 55 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.19e-02 7.06e+03 6.26e+00 bond pdb=" N ILE P 56 " pdb=" CA ILE P 56 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.76e+00 bond pdb=" N ASP P 54 " pdb=" CA ASP P 54 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.16e-02 7.43e+03 4.23e+00 bond pdb=" CB GLU E 274 " pdb=" CG GLU E 274 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB LYS G 165 " pdb=" CG LYS G 165 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 ... (remaining 17685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 23369 1.80 - 3.59: 432 3.59 - 5.39: 95 5.39 - 7.18: 10 7.18 - 8.98: 3 Bond angle restraints: 23909 Sorted by residual: angle pdb=" N VAL A 72 " pdb=" CA VAL A 72 " pdb=" C VAL A 72 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CA GLU D 165 " pdb=" CB GLU D 165 " pdb=" CG GLU D 165 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CB LYS G 165 " pdb=" CG LYS G 165 " pdb=" CD LYS G 165 " ideal model delta sigma weight residual 111.30 118.70 -7.40 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CA ASP P 54 " pdb=" CB ASP P 54 " pdb=" CG ASP P 54 " ideal model delta sigma weight residual 112.60 115.80 -3.20 1.00e+00 1.00e+00 1.03e+01 angle pdb=" N GLY E 87 " pdb=" CA GLY E 87 " pdb=" C GLY E 87 " ideal model delta sigma weight residual 113.18 105.61 7.57 2.37e+00 1.78e-01 1.02e+01 ... (remaining 23904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9206 18.00 - 36.00: 1103 36.00 - 53.99: 342 53.99 - 71.99: 97 71.99 - 89.99: 28 Dihedral angle restraints: 10776 sinusoidal: 4359 harmonic: 6417 Sorted by residual: dihedral pdb=" CA GLY E 87 " pdb=" C GLY E 87 " pdb=" N GLU E 88 " pdb=" CA GLU E 88 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA VAL E 85 " pdb=" C VAL E 85 " pdb=" N ASP E 86 " pdb=" CA ASP E 86 " ideal model delta harmonic sigma weight residual 180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ALA C 152 " pdb=" C ALA C 152 " pdb=" N LYS C 153 " pdb=" CA LYS C 153 " ideal model delta harmonic sigma weight residual 180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 10773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1973 0.037 - 0.073: 580 0.073 - 0.110: 115 0.110 - 0.146: 50 0.146 - 0.183: 1 Chirality restraints: 2719 Sorted by residual: chirality pdb=" CA ILE P 56 " pdb=" N ILE P 56 " pdb=" C ILE P 56 " pdb=" CB ILE P 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA ILE F 99 " pdb=" N ILE F 99 " pdb=" C ILE F 99 " pdb=" CB ILE F 99 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA VAL F 250 " pdb=" N VAL F 250 " pdb=" C VAL F 250 " pdb=" CB VAL F 250 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2716 not shown) Planarity restraints: 3060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 207 " 0.225 9.50e-02 1.11e+02 1.01e-01 6.94e+00 pdb=" NE ARG D 207 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 207 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 207 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 207 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 182 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" CD GLN D 182 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN D 182 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN D 182 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 254 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO C 255 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 255 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 255 " -0.028 5.00e-02 4.00e+02 ... (remaining 3057 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 3 2.16 - 2.84: 5689 2.84 - 3.53: 23704 3.53 - 4.21: 35507 4.21 - 4.90: 66635 Nonbonded interactions: 131538 Sorted by model distance: nonbonded pdb="ZN ZN E 401 " pdb=" O HOH E 501 " model vdw 1.474 2.230 nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 401 " model vdw 1.698 2.230 nonbonded pdb=" O SER H 157 " pdb=" OG1 THR H 158 " model vdw 2.153 3.040 nonbonded pdb=" NZ LYS D 251 " pdb=" OE2 GLU F 169 " model vdw 2.217 3.120 nonbonded pdb=" N GLU G 83 " pdb=" OE1 GLU G 83 " model vdw 2.228 3.120 ... (remaining 131533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17692 Z= 0.192 Angle : 0.631 8.981 23909 Z= 0.333 Chirality : 0.038 0.183 2719 Planarity : 0.005 0.101 3060 Dihedral : 18.286 89.989 6612 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.68 % Allowed : 24.51 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2147 helix: 1.41 (0.14), residues: 1405 sheet: -0.74 (0.43), residues: 153 loop : -1.89 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 207 TYR 0.013 0.001 TYR C 227 PHE 0.014 0.002 PHE F 309 TRP 0.009 0.001 TRP E 242 HIS 0.011 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00450 (17690) covalent geometry : angle 0.63144 (23909) hydrogen bonds : bond 0.18021 ( 1045) hydrogen bonds : angle 5.43580 ( 3069) metal coordination : bond 0.04335 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 446 time to evaluate : 0.594 Fit side-chains REVERT: E 30 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8103 (ttpp) REVERT: E 180 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8324 (ptmm) REVERT: E 220 GLN cc_start: 0.8240 (mt0) cc_final: 0.7989 (mt0) REVERT: E 319 MET cc_start: 0.8036 (mtm) cc_final: 0.7800 (mtm) REVERT: A 65 ASP cc_start: 0.7471 (t0) cc_final: 0.7260 (t0) REVERT: A 137 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7753 (mmtm) REVERT: A 183 LYS cc_start: 0.7723 (tptt) cc_final: 0.7351 (tptt) REVERT: A 257 GLU cc_start: 0.7480 (pm20) cc_final: 0.7180 (pm20) REVERT: A 309 ASN cc_start: 0.8285 (m110) cc_final: 0.7805 (m110) REVERT: A 351 ASN cc_start: 0.8740 (m-40) cc_final: 0.8503 (m-40) REVERT: A 447 GLN cc_start: 0.8388 (mt0) cc_final: 0.8071 (mt0) REVERT: A 451 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7846 (mtpp) REVERT: B 338 MET cc_start: 0.6922 (mmm) cc_final: 0.6609 (mmm) REVERT: C 10 ASN cc_start: 0.7870 (t0) cc_final: 0.7601 (m110) REVERT: C 56 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8172 (mp) REVERT: C 89 ASN cc_start: 0.7708 (t0) cc_final: 0.7265 (t0) REVERT: C 156 LYS cc_start: 0.8197 (tttt) cc_final: 0.7997 (tttt) REVERT: C 247 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7779 (mm-40) REVERT: D 198 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7253 (ttp80) REVERT: D 253 GLU cc_start: 0.8134 (tp30) cc_final: 0.7775 (tp30) REVERT: F 144 GLU cc_start: 0.8343 (tt0) cc_final: 0.8019 (mt-10) REVERT: F 246 GLU cc_start: 0.7869 (tp30) cc_final: 0.7446 (tp30) REVERT: G 14 GLN cc_start: 0.7349 (mm110) cc_final: 0.7131 (mm110) REVERT: H 103 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.5918 (tm130) REVERT: H 137 VAL cc_start: 0.7885 (m) cc_final: 0.7483 (t) outliers start: 32 outliers final: 21 residues processed: 465 average time/residue: 0.7329 time to fit residues: 371.7837 Evaluate side-chains 451 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 427 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0570 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN E 158 ASN E 182 ASN E 248 ASN E 258 ASN E 330 GLN A 204 ASN B 436 GLN C 136 ASN C 271 ASN C 282 HIS C 368 ASN C 369 ASN C 395 GLN F 80 ASN F 155 ASN H 39 GLN H 47 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116145 restraints weight = 24557.146| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.14 r_work: 0.3392 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17692 Z= 0.148 Angle : 0.542 7.274 23909 Z= 0.288 Chirality : 0.039 0.138 2719 Planarity : 0.004 0.050 3060 Dihedral : 5.989 81.997 2398 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.10 % Allowed : 22.94 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2147 helix: 1.67 (0.14), residues: 1443 sheet: -0.43 (0.42), residues: 153 loop : -1.88 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 207 TYR 0.013 0.001 TYR C 244 PHE 0.015 0.001 PHE E 96 TRP 0.008 0.001 TRP E 146 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00323 (17690) covalent geometry : angle 0.54217 (23909) hydrogen bonds : bond 0.06167 ( 1045) hydrogen bonds : angle 4.00291 ( 3069) metal coordination : bond 0.00716 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 419 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 258 ASN cc_start: 0.6580 (OUTLIER) cc_final: 0.6076 (p0) REVERT: E 309 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7613 (ttmm) REVERT: E 319 MET cc_start: 0.8292 (mtm) cc_final: 0.8059 (mtm) REVERT: A 65 ASP cc_start: 0.7488 (t0) cc_final: 0.7260 (t0) REVERT: A 257 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: A 280 PHE cc_start: 0.7440 (m-10) cc_final: 0.7146 (m-10) REVERT: A 305 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 309 ASN cc_start: 0.8156 (m110) cc_final: 0.7554 (m110) REVERT: A 317 LYS cc_start: 0.8039 (tppt) cc_final: 0.7428 (tppt) REVERT: A 351 ASN cc_start: 0.8765 (m-40) cc_final: 0.8532 (m-40) REVERT: A 447 GLN cc_start: 0.8419 (mt0) cc_final: 0.8135 (mt0) REVERT: B 334 HIS cc_start: 0.4994 (OUTLIER) cc_final: 0.4753 (m90) REVERT: B 338 MET cc_start: 0.6806 (mmm) cc_final: 0.6488 (mmm) REVERT: C 10 ASN cc_start: 0.7836 (t0) cc_final: 0.7469 (m110) REVERT: C 89 ASN cc_start: 0.7597 (t0) cc_final: 0.7170 (t0) REVERT: C 156 LYS cc_start: 0.8274 (mttt) cc_final: 0.8046 (tttt) REVERT: C 168 ASP cc_start: 0.7734 (m-30) cc_final: 0.7521 (t0) REVERT: C 247 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7848 (mm-40) REVERT: C 312 LYS cc_start: 0.8615 (mttt) cc_final: 0.8346 (mtpp) REVERT: C 373 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6523 (mt) REVERT: D 198 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7179 (ttp80) REVERT: D 253 GLU cc_start: 0.8224 (tp30) cc_final: 0.7782 (tp30) REVERT: D 256 GLN cc_start: 0.8535 (mt0) cc_final: 0.8221 (mt0) REVERT: F 77 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7506 (tm-30) REVERT: F 144 GLU cc_start: 0.8434 (tt0) cc_final: 0.8090 (mt-10) REVERT: F 246 GLU cc_start: 0.7907 (tp30) cc_final: 0.7569 (tp30) REVERT: G 14 GLN cc_start: 0.7486 (mm110) cc_final: 0.7182 (mm110) REVERT: G 87 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7776 (pp20) REVERT: H 107 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: H 137 VAL cc_start: 0.7805 (m) cc_final: 0.7431 (t) REVERT: P 47 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: P 55 ASP cc_start: 0.8171 (t70) cc_final: 0.7822 (t0) outliers start: 78 outliers final: 37 residues processed: 465 average time/residue: 0.7489 time to fit residues: 379.5389 Evaluate side-chains 450 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 407 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 136 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 91 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 258 ASN E 330 GLN A 155 ASN A 171 HIS A 204 ASN A 288 ASN A 431 GLN B 436 GLN C 136 ASN C 282 HIS C 395 GLN D 182 GLN D 206 GLN D 373 GLN D 390 GLN F 155 ASN G 81 ASN H 39 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115819 restraints weight = 25019.691| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.15 r_work: 0.3392 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17692 Z= 0.142 Angle : 0.521 6.962 23909 Z= 0.273 Chirality : 0.039 0.140 2719 Planarity : 0.004 0.051 3060 Dihedral : 5.069 58.315 2370 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.47 % Allowed : 23.72 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2147 helix: 1.80 (0.14), residues: 1447 sheet: -0.28 (0.43), residues: 153 loop : -1.94 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 207 TYR 0.014 0.001 TYR C 244 PHE 0.016 0.001 PHE E 96 TRP 0.007 0.001 TRP F 124 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00318 (17690) covalent geometry : angle 0.52057 (23909) hydrogen bonds : bond 0.05669 ( 1045) hydrogen bonds : angle 3.80613 ( 3069) metal coordination : bond 0.00683 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 416 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 48 ASP cc_start: 0.8267 (t0) cc_final: 0.7965 (t0) REVERT: E 239 GLU cc_start: 0.8315 (tp30) cc_final: 0.7987 (tp30) REVERT: E 274 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7576 (tm-30) REVERT: E 309 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7639 (ttmm) REVERT: E 319 MET cc_start: 0.8430 (mtm) cc_final: 0.8155 (mtm) REVERT: A 65 ASP cc_start: 0.7517 (t0) cc_final: 0.7288 (t0) REVERT: A 183 LYS cc_start: 0.7959 (tptt) cc_final: 0.7550 (tptt) REVERT: A 191 TYR cc_start: 0.4816 (OUTLIER) cc_final: 0.4335 (t80) REVERT: A 257 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: A 280 PHE cc_start: 0.7488 (m-10) cc_final: 0.7106 (m-10) REVERT: A 305 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 309 ASN cc_start: 0.8143 (m110) cc_final: 0.7524 (m110) REVERT: A 317 LYS cc_start: 0.8009 (tppt) cc_final: 0.7383 (tppt) REVERT: A 351 ASN cc_start: 0.8761 (m-40) cc_final: 0.8532 (m-40) REVERT: A 422 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7831 (mmtt) REVERT: A 447 GLN cc_start: 0.8440 (mt0) cc_final: 0.8232 (mt0) REVERT: B 338 MET cc_start: 0.6453 (mmm) cc_final: 0.5518 (mtt) REVERT: C 10 ASN cc_start: 0.7836 (t0) cc_final: 0.7471 (m110) REVERT: C 39 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6776 (mp) REVERT: C 89 ASN cc_start: 0.7569 (t0) cc_final: 0.7138 (t0) REVERT: C 115 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7831 (mmmm) REVERT: C 156 LYS cc_start: 0.8243 (mttt) cc_final: 0.7984 (tttt) REVERT: C 247 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7881 (mm-40) REVERT: C 312 LYS cc_start: 0.8613 (mttt) cc_final: 0.8348 (mtpp) REVERT: C 350 SER cc_start: 0.8407 (p) cc_final: 0.8200 (m) REVERT: C 373 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6496 (mt) REVERT: D 198 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7130 (ttp80) REVERT: D 253 GLU cc_start: 0.8195 (tp30) cc_final: 0.7755 (tp30) REVERT: D 256 GLN cc_start: 0.8525 (mt0) cc_final: 0.8222 (mt0) REVERT: D 286 MET cc_start: 0.8016 (mmm) cc_final: 0.7579 (mmm) REVERT: D 336 GLU cc_start: 0.7775 (tt0) cc_final: 0.7446 (tt0) REVERT: F 77 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7529 (tm-30) REVERT: F 144 GLU cc_start: 0.8431 (tt0) cc_final: 0.8101 (mt-10) REVERT: F 246 GLU cc_start: 0.7941 (tp30) cc_final: 0.7567 (tp30) REVERT: F 308 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8046 (ttmm) REVERT: G 14 GLN cc_start: 0.7532 (mm110) cc_final: 0.7246 (mm110) REVERT: G 36 GLU cc_start: 0.7671 (tt0) cc_final: 0.6938 (tm-30) REVERT: G 87 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7792 (pp20) REVERT: H 103 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5693 (tt0) REVERT: H 107 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: H 137 VAL cc_start: 0.7787 (m) cc_final: 0.7475 (t) REVERT: P 55 ASP cc_start: 0.8160 (t70) cc_final: 0.7809 (t0) outliers start: 85 outliers final: 47 residues processed: 470 average time/residue: 0.7115 time to fit residues: 365.7770 Evaluate side-chains 458 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 404 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 75 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 155 ASN A 204 ASN A 431 GLN B 436 GLN C 136 ASN C 282 HIS C 290 ASN D 206 GLN F 155 ASN G 81 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115913 restraints weight = 24776.103| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.14 r_work: 0.3386 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17692 Z= 0.152 Angle : 0.525 7.194 23909 Z= 0.274 Chirality : 0.039 0.144 2719 Planarity : 0.004 0.052 3060 Dihedral : 5.071 58.098 2368 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.10 % Allowed : 23.72 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 2147 helix: 1.86 (0.14), residues: 1442 sheet: -0.20 (0.42), residues: 163 loop : -1.99 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 207 TYR 0.015 0.001 TYR C 244 PHE 0.017 0.001 PHE E 96 TRP 0.010 0.001 TRP F 124 HIS 0.008 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00351 (17690) covalent geometry : angle 0.52541 (23909) hydrogen bonds : bond 0.05641 ( 1045) hydrogen bonds : angle 3.72693 ( 3069) metal coordination : bond 0.00633 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 402 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 227 SER cc_start: 0.8685 (m) cc_final: 0.8383 (t) REVERT: E 239 GLU cc_start: 0.8301 (tp30) cc_final: 0.7943 (tp30) REVERT: E 274 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7581 (tm-30) REVERT: E 309 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7698 (ttmm) REVERT: E 319 MET cc_start: 0.8482 (mtm) cc_final: 0.8244 (mtm) REVERT: E 330 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: A 65 ASP cc_start: 0.7526 (t0) cc_final: 0.7319 (t0) REVERT: A 183 LYS cc_start: 0.7979 (tptt) cc_final: 0.7557 (tptt) REVERT: A 191 TYR cc_start: 0.4816 (OUTLIER) cc_final: 0.4310 (t80) REVERT: A 257 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: A 280 PHE cc_start: 0.7554 (m-10) cc_final: 0.7131 (m-10) REVERT: A 283 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6902 (pp) REVERT: A 292 TYR cc_start: 0.7463 (m-10) cc_final: 0.7207 (m-10) REVERT: A 305 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 309 ASN cc_start: 0.8143 (m110) cc_final: 0.7516 (m110) REVERT: A 317 LYS cc_start: 0.7999 (tppt) cc_final: 0.7380 (tppt) REVERT: A 351 ASN cc_start: 0.8770 (m-40) cc_final: 0.8545 (m-40) REVERT: A 422 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7792 (mmtt) REVERT: A 447 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: B 338 MET cc_start: 0.6327 (mmm) cc_final: 0.5559 (mtt) REVERT: B 436 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: C 10 ASN cc_start: 0.7836 (t0) cc_final: 0.7469 (m110) REVERT: C 39 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6791 (mp) REVERT: C 89 ASN cc_start: 0.7538 (t0) cc_final: 0.7114 (t0) REVERT: C 98 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: C 115 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7862 (mmmm) REVERT: C 123 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6918 (mt) REVERT: C 156 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7960 (tttt) REVERT: C 247 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7898 (mm-40) REVERT: C 312 LYS cc_start: 0.8615 (mttt) cc_final: 0.8356 (mtpp) REVERT: C 350 SER cc_start: 0.8405 (p) cc_final: 0.8204 (m) REVERT: C 395 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: D 198 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7122 (ttp80) REVERT: D 214 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7462 (mmtt) REVERT: D 248 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8373 (t) REVERT: D 253 GLU cc_start: 0.8185 (tp30) cc_final: 0.7741 (tp30) REVERT: D 256 GLN cc_start: 0.8523 (mt0) cc_final: 0.8213 (mt0) REVERT: D 286 MET cc_start: 0.8011 (mmm) cc_final: 0.7574 (mmm) REVERT: D 336 GLU cc_start: 0.7783 (tt0) cc_final: 0.7491 (tt0) REVERT: F 77 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7544 (tm-30) REVERT: F 144 GLU cc_start: 0.8409 (tt0) cc_final: 0.8072 (mt-10) REVERT: F 175 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8052 (OUTLIER) REVERT: F 246 GLU cc_start: 0.7942 (tp30) cc_final: 0.7588 (tp30) REVERT: F 308 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8038 (ttmm) REVERT: G 14 GLN cc_start: 0.7585 (mm110) cc_final: 0.7314 (mm110) REVERT: G 36 GLU cc_start: 0.7646 (tt0) cc_final: 0.6925 (tm-30) REVERT: G 87 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7786 (pp20) REVERT: H 103 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.5689 (tt0) REVERT: H 106 MET cc_start: 0.7269 (mmm) cc_final: 0.6973 (mtm) REVERT: H 107 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: H 137 VAL cc_start: 0.7780 (m) cc_final: 0.7465 (t) REVERT: P 55 ASP cc_start: 0.8100 (t70) cc_final: 0.7782 (t0) outliers start: 97 outliers final: 53 residues processed: 458 average time/residue: 0.7252 time to fit residues: 362.3165 Evaluate side-chains 467 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 399 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 234 ASP Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 431 GLN B 436 GLN C 136 ASN C 282 HIS D 182 GLN D 206 GLN F 155 ASN G 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115660 restraints weight = 24655.903| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.13 r_work: 0.3394 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17692 Z= 0.144 Angle : 0.518 8.078 23909 Z= 0.270 Chirality : 0.039 0.133 2719 Planarity : 0.004 0.051 3060 Dihedral : 5.041 57.908 2368 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.79 % Allowed : 24.46 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2147 helix: 1.92 (0.14), residues: 1443 sheet: -0.18 (0.42), residues: 163 loop : -1.98 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 207 TYR 0.014 0.001 TYR C 244 PHE 0.016 0.001 PHE E 96 TRP 0.013 0.001 TRP F 124 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00331 (17690) covalent geometry : angle 0.51816 (23909) hydrogen bonds : bond 0.05435 ( 1045) hydrogen bonds : angle 3.65816 ( 3069) metal coordination : bond 0.00466 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 409 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 MET cc_start: 0.8413 (mpp) cc_final: 0.7870 (mpp) REVERT: E 227 SER cc_start: 0.8676 (m) cc_final: 0.8394 (t) REVERT: E 239 GLU cc_start: 0.8283 (tp30) cc_final: 0.7954 (tp30) REVERT: E 274 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7731 (tm-30) REVERT: E 309 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7715 (ttmm) REVERT: E 319 MET cc_start: 0.8499 (mtm) cc_final: 0.8267 (mtm) REVERT: E 330 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: A 65 ASP cc_start: 0.7532 (t0) cc_final: 0.7326 (t0) REVERT: A 183 LYS cc_start: 0.7979 (tptt) cc_final: 0.7573 (tptt) REVERT: A 191 TYR cc_start: 0.4835 (OUTLIER) cc_final: 0.4320 (t80) REVERT: A 196 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7201 (pmtt) REVERT: A 201 MET cc_start: 0.7293 (tmm) cc_final: 0.7074 (tmm) REVERT: A 248 LYS cc_start: 0.5671 (pmtt) cc_final: 0.4795 (tttt) REVERT: A 257 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: A 280 PHE cc_start: 0.7612 (m-10) cc_final: 0.7206 (m-10) REVERT: A 305 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 309 ASN cc_start: 0.8142 (m110) cc_final: 0.7513 (m110) REVERT: A 351 ASN cc_start: 0.8765 (m-40) cc_final: 0.8543 (m-40) REVERT: A 422 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: A 447 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: C 10 ASN cc_start: 0.7836 (t0) cc_final: 0.7473 (m110) REVERT: C 39 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6806 (mp) REVERT: C 89 ASN cc_start: 0.7515 (t0) cc_final: 0.7097 (t0) REVERT: C 98 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: C 115 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7866 (mmmm) REVERT: C 123 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6922 (mt) REVERT: C 156 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7982 (mttt) REVERT: C 247 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7905 (mm-40) REVERT: C 312 LYS cc_start: 0.8629 (mttt) cc_final: 0.8377 (mtpp) REVERT: C 395 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: D 198 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7110 (ttp80) REVERT: D 214 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7404 (mmtt) REVERT: D 248 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8367 (t) REVERT: D 253 GLU cc_start: 0.8196 (tp30) cc_final: 0.7759 (tp30) REVERT: D 256 GLN cc_start: 0.8520 (mt0) cc_final: 0.8209 (mt0) REVERT: D 286 MET cc_start: 0.7982 (mmm) cc_final: 0.7550 (mmm) REVERT: F 77 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7553 (tm-30) REVERT: F 144 GLU cc_start: 0.8402 (tt0) cc_final: 0.8065 (mt-10) REVERT: F 175 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (mt) REVERT: F 246 GLU cc_start: 0.7937 (tp30) cc_final: 0.7579 (tp30) REVERT: F 261 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8169 (t80) REVERT: F 308 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8014 (ttmm) REVERT: G 14 GLN cc_start: 0.7588 (mm110) cc_final: 0.7323 (mm110) REVERT: G 36 GLU cc_start: 0.7628 (tt0) cc_final: 0.6907 (tm-30) REVERT: G 87 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7774 (pp20) REVERT: H 16 LEU cc_start: 0.7642 (tm) cc_final: 0.7396 (tt) REVERT: H 103 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: H 107 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: H 110 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7249 (ttp80) REVERT: H 137 VAL cc_start: 0.7770 (m) cc_final: 0.7464 (t) REVERT: P 55 ASP cc_start: 0.8114 (t70) cc_final: 0.7765 (t0) outliers start: 91 outliers final: 58 residues processed: 465 average time/residue: 0.7304 time to fit residues: 370.9219 Evaluate side-chains 478 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 404 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 43 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN B 436 GLN C 136 ASN C 282 HIS C 395 GLN D 206 GLN F 155 ASN G 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115256 restraints weight = 25084.591| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.22 r_work: 0.3358 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17692 Z= 0.155 Angle : 0.528 7.556 23909 Z= 0.275 Chirality : 0.039 0.135 2719 Planarity : 0.004 0.052 3060 Dihedral : 5.075 57.797 2368 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.31 % Allowed : 24.51 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2147 helix: 1.92 (0.14), residues: 1443 sheet: -0.17 (0.42), residues: 163 loop : -1.96 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 207 TYR 0.016 0.001 TYR C 244 PHE 0.017 0.001 PHE E 96 TRP 0.018 0.001 TRP F 124 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00361 (17690) covalent geometry : angle 0.52796 (23909) hydrogen bonds : bond 0.05566 ( 1045) hydrogen bonds : angle 3.63130 ( 3069) metal coordination : bond 0.00479 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 408 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 MET cc_start: 0.8367 (mpp) cc_final: 0.7873 (mpp) REVERT: E 227 SER cc_start: 0.8679 (m) cc_final: 0.8369 (t) REVERT: E 239 GLU cc_start: 0.8331 (tp30) cc_final: 0.8008 (tp30) REVERT: E 274 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 309 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7692 (ttmm) REVERT: E 319 MET cc_start: 0.8473 (mtm) cc_final: 0.8257 (mtm) REVERT: E 330 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: A 65 ASP cc_start: 0.7556 (t0) cc_final: 0.7288 (t0) REVERT: A 83 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: A 183 LYS cc_start: 0.7935 (tptt) cc_final: 0.7533 (tptt) REVERT: A 191 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4240 (t80) REVERT: A 196 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7155 (pmtt) REVERT: A 201 MET cc_start: 0.7379 (tmm) cc_final: 0.7141 (tmm) REVERT: A 248 LYS cc_start: 0.5821 (pmtt) cc_final: 0.4953 (tttt) REVERT: A 257 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: A 258 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7186 (tp) REVERT: A 280 PHE cc_start: 0.7648 (m-10) cc_final: 0.7203 (m-10) REVERT: A 305 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 309 ASN cc_start: 0.8051 (m110) cc_final: 0.7427 (m110) REVERT: A 351 ASN cc_start: 0.8801 (m-40) cc_final: 0.8565 (m-40) REVERT: A 422 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7846 (mmtt) REVERT: A 447 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: C 10 ASN cc_start: 0.7805 (t0) cc_final: 0.7435 (m110) REVERT: C 115 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7856 (mmmm) REVERT: C 123 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6893 (mt) REVERT: C 156 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7962 (mttt) REVERT: C 247 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7802 (mm-40) REVERT: C 312 LYS cc_start: 0.8604 (mttt) cc_final: 0.8326 (mtpp) REVERT: D 198 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7045 (ttp80) REVERT: D 248 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8297 (t) REVERT: D 253 GLU cc_start: 0.8221 (tp30) cc_final: 0.7747 (tp30) REVERT: D 256 GLN cc_start: 0.8538 (mt0) cc_final: 0.8220 (mt0) REVERT: D 286 MET cc_start: 0.8046 (mmm) cc_final: 0.7574 (mmm) REVERT: F 77 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7448 (tm-30) REVERT: F 144 GLU cc_start: 0.8378 (tt0) cc_final: 0.8036 (mt-10) REVERT: F 175 ILE cc_start: 0.8202 (tp) cc_final: 0.7952 (OUTLIER) REVERT: F 246 GLU cc_start: 0.7959 (tp30) cc_final: 0.7642 (tp30) REVERT: F 261 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.8135 (t80) REVERT: F 308 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7979 (ttmm) REVERT: G 14 GLN cc_start: 0.7527 (mm110) cc_final: 0.7277 (mm110) REVERT: G 36 GLU cc_start: 0.7570 (tt0) cc_final: 0.6811 (tm-30) REVERT: G 87 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7757 (pp20) REVERT: H 103 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5638 (tt0) REVERT: H 106 MET cc_start: 0.7236 (mmm) cc_final: 0.7017 (mtm) REVERT: H 107 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: H 137 VAL cc_start: 0.7663 (m) cc_final: 0.7343 (t) REVERT: P 55 ASP cc_start: 0.8141 (t70) cc_final: 0.7769 (t0) outliers start: 101 outliers final: 63 residues processed: 470 average time/residue: 0.7209 time to fit residues: 369.4828 Evaluate side-chains 480 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 404 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 142 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 134 optimal weight: 0.0010 chunk 185 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN B 436 GLN C 136 ASN C 282 HIS D 206 GLN F 80 ASN F 155 ASN G 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114674 restraints weight = 25036.323| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.28 r_work: 0.3374 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17692 Z= 0.133 Angle : 0.515 9.087 23909 Z= 0.267 Chirality : 0.038 0.196 2719 Planarity : 0.004 0.050 3060 Dihedral : 4.916 57.502 2366 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.05 % Allowed : 24.78 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 2147 helix: 1.99 (0.14), residues: 1450 sheet: -0.21 (0.41), residues: 167 loop : -2.01 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 207 TYR 0.015 0.001 TYR C 244 PHE 0.014 0.001 PHE E 96 TRP 0.020 0.001 TRP F 124 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00299 (17690) covalent geometry : angle 0.51534 (23909) hydrogen bonds : bond 0.05090 ( 1045) hydrogen bonds : angle 3.54639 ( 3069) metal coordination : bond 0.00320 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 406 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 227 SER cc_start: 0.8659 (m) cc_final: 0.8362 (t) REVERT: E 239 GLU cc_start: 0.8360 (tp30) cc_final: 0.8021 (tp30) REVERT: E 274 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7702 (tm-30) REVERT: E 309 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7685 (ttmm) REVERT: E 319 MET cc_start: 0.8469 (mtm) cc_final: 0.8242 (mtm) REVERT: E 330 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: A 65 ASP cc_start: 0.7577 (t0) cc_final: 0.7319 (t0) REVERT: A 183 LYS cc_start: 0.7959 (tptt) cc_final: 0.7536 (tptt) REVERT: A 191 TYR cc_start: 0.4758 (OUTLIER) cc_final: 0.4198 (t80) REVERT: A 196 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7176 (pmtt) REVERT: A 201 MET cc_start: 0.7369 (tmm) cc_final: 0.7121 (tmm) REVERT: A 248 LYS cc_start: 0.5578 (pmtt) cc_final: 0.4800 (tttp) REVERT: A 257 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 258 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7225 (OUTLIER) REVERT: A 280 PHE cc_start: 0.7583 (m-10) cc_final: 0.7232 (m-10) REVERT: A 305 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 309 ASN cc_start: 0.8067 (m110) cc_final: 0.7444 (m110) REVERT: A 351 ASN cc_start: 0.8778 (m-40) cc_final: 0.8549 (m-40) REVERT: A 368 GLN cc_start: 0.8525 (mt0) cc_final: 0.8274 (mt0) REVERT: A 422 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7839 (mmtt) REVERT: A 447 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: C 10 ASN cc_start: 0.7792 (t0) cc_final: 0.7423 (m110) REVERT: C 54 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7974 (m90) REVERT: C 115 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7850 (mmmm) REVERT: C 123 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6852 (mt) REVERT: C 156 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7971 (mttt) REVERT: C 167 MET cc_start: 0.8309 (mmt) cc_final: 0.8096 (mmm) REVERT: C 247 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7764 (mm-40) REVERT: C 312 LYS cc_start: 0.8602 (mttt) cc_final: 0.8336 (mtpp) REVERT: C 328 LEU cc_start: 0.8418 (mt) cc_final: 0.8202 (mt) REVERT: C 395 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: D 198 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7002 (ttp80) REVERT: D 253 GLU cc_start: 0.8233 (tp30) cc_final: 0.7765 (tp30) REVERT: D 256 GLN cc_start: 0.8473 (mt0) cc_final: 0.8145 (mt0) REVERT: D 286 MET cc_start: 0.8074 (mmm) cc_final: 0.7590 (mmm) REVERT: F 77 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7450 (tm-30) REVERT: F 144 GLU cc_start: 0.8368 (tt0) cc_final: 0.8028 (mt-10) REVERT: F 175 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7950 (OUTLIER) REVERT: F 246 GLU cc_start: 0.7952 (tp30) cc_final: 0.7626 (tp30) REVERT: F 308 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7914 (ttmm) REVERT: G 14 GLN cc_start: 0.7543 (mm110) cc_final: 0.7281 (mm110) REVERT: G 36 GLU cc_start: 0.7527 (tt0) cc_final: 0.6792 (tm-30) REVERT: G 87 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7756 (pp20) REVERT: H 16 LEU cc_start: 0.7617 (tm) cc_final: 0.7390 (tt) REVERT: H 103 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5575 (tt0) REVERT: H 107 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: H 110 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7122 (ttp80) REVERT: H 137 VAL cc_start: 0.7581 (m) cc_final: 0.7300 (t) REVERT: H 199 ARG cc_start: 0.7451 (mmm-85) cc_final: 0.7104 (mmm160) REVERT: P 55 ASP cc_start: 0.8098 (t70) cc_final: 0.7747 (t0) outliers start: 96 outliers final: 61 residues processed: 463 average time/residue: 0.7237 time to fit residues: 366.2645 Evaluate side-chains 480 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 407 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 177 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 166 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 194 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 431 GLN B 436 GLN C 136 ASN C 282 HIS D 206 GLN F 155 ASN G 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114237 restraints weight = 25081.204| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.30 r_work: 0.3368 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17692 Z= 0.139 Angle : 0.517 7.880 23909 Z= 0.268 Chirality : 0.039 0.180 2719 Planarity : 0.004 0.051 3060 Dihedral : 4.920 58.145 2366 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.63 % Allowed : 25.41 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2147 helix: 1.98 (0.14), residues: 1457 sheet: -0.19 (0.41), residues: 167 loop : -1.99 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 207 TYR 0.015 0.001 TYR C 244 PHE 0.015 0.001 PHE E 96 TRP 0.026 0.001 TRP F 124 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00321 (17690) covalent geometry : angle 0.51708 (23909) hydrogen bonds : bond 0.05169 ( 1045) hydrogen bonds : angle 3.53215 ( 3069) metal coordination : bond 0.00371 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 407 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 227 SER cc_start: 0.8663 (m) cc_final: 0.8364 (t) REVERT: E 239 GLU cc_start: 0.8377 (tp30) cc_final: 0.8044 (tp30) REVERT: E 254 SER cc_start: 0.8149 (t) cc_final: 0.7913 (t) REVERT: E 274 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7731 (tm-30) REVERT: E 309 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7684 (ttmm) REVERT: E 319 MET cc_start: 0.8470 (mtm) cc_final: 0.8241 (mtm) REVERT: A 65 ASP cc_start: 0.7581 (t0) cc_final: 0.7335 (t0) REVERT: A 90 MET cc_start: 0.6157 (mmp) cc_final: 0.5935 (mmp) REVERT: A 191 TYR cc_start: 0.4759 (OUTLIER) cc_final: 0.4231 (t80) REVERT: A 196 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7183 (pmtt) REVERT: A 201 MET cc_start: 0.7367 (tmm) cc_final: 0.7091 (tmm) REVERT: A 248 LYS cc_start: 0.5636 (pmtt) cc_final: 0.4854 (tttp) REVERT: A 257 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: A 280 PHE cc_start: 0.7594 (m-10) cc_final: 0.7293 (m-10) REVERT: A 305 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 309 ASN cc_start: 0.8079 (m110) cc_final: 0.7450 (m110) REVERT: A 317 LYS cc_start: 0.7982 (tppt) cc_final: 0.7313 (tppt) REVERT: A 351 ASN cc_start: 0.8775 (m-40) cc_final: 0.8546 (m-40) REVERT: A 368 GLN cc_start: 0.8527 (mt0) cc_final: 0.8273 (mt0) REVERT: A 447 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: C 10 ASN cc_start: 0.7798 (t0) cc_final: 0.7428 (m110) REVERT: C 115 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7864 (mmtm) REVERT: C 123 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6880 (mt) REVERT: C 156 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7978 (mttt) REVERT: C 247 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7766 (mm-40) REVERT: C 312 LYS cc_start: 0.8613 (mttt) cc_final: 0.8347 (mtpp) REVERT: C 313 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8166 (t) REVERT: C 328 LEU cc_start: 0.8423 (mt) cc_final: 0.8210 (mt) REVERT: C 395 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: D 155 TYR cc_start: 0.6450 (m-10) cc_final: 0.6240 (m-10) REVERT: D 198 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7021 (ttp80) REVERT: D 253 GLU cc_start: 0.8231 (tp30) cc_final: 0.7733 (tp30) REVERT: D 256 GLN cc_start: 0.8478 (mt0) cc_final: 0.8113 (mt0) REVERT: D 286 MET cc_start: 0.8098 (mmm) cc_final: 0.7618 (mmm) REVERT: F 77 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7464 (tm-30) REVERT: F 144 GLU cc_start: 0.8389 (tt0) cc_final: 0.8052 (mt-10) REVERT: F 246 GLU cc_start: 0.7971 (tp30) cc_final: 0.7649 (tp30) REVERT: F 261 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8152 (t80) REVERT: F 308 LYS cc_start: 0.8309 (ttmm) cc_final: 0.7922 (ttmm) REVERT: G 14 GLN cc_start: 0.7556 (mm110) cc_final: 0.7314 (mm110) REVERT: G 36 GLU cc_start: 0.7545 (tt0) cc_final: 0.6845 (tm-30) REVERT: G 87 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7759 (OUTLIER) REVERT: G 147 GLN cc_start: 0.8151 (tp40) cc_final: 0.7753 (tt0) REVERT: G 165 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8437 (mmmt) REVERT: H 16 LEU cc_start: 0.7591 (tm) cc_final: 0.7363 (tt) REVERT: H 107 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: H 137 VAL cc_start: 0.7566 (m) cc_final: 0.7289 (t) REVERT: H 199 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.7102 (mmm160) REVERT: P 55 ASP cc_start: 0.8111 (t70) cc_final: 0.7762 (t0) outliers start: 88 outliers final: 61 residues processed: 463 average time/residue: 0.7182 time to fit residues: 363.4394 Evaluate side-chains 475 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 405 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 185 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS A 431 GLN B 436 GLN C 136 ASN C 147 GLN C 282 HIS D 206 GLN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN F 155 ASN G 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114592 restraints weight = 25157.269| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.30 r_work: 0.3372 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17692 Z= 0.135 Angle : 0.522 7.866 23909 Z= 0.271 Chirality : 0.039 0.160 2719 Planarity : 0.004 0.050 3060 Dihedral : 4.928 58.601 2366 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.37 % Allowed : 26.09 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 2147 helix: 2.00 (0.14), residues: 1457 sheet: -0.15 (0.42), residues: 167 loop : -1.96 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 207 TYR 0.015 0.001 TYR C 244 PHE 0.014 0.001 PHE E 96 TRP 0.029 0.001 TRP F 124 HIS 0.006 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00307 (17690) covalent geometry : angle 0.52242 (23909) hydrogen bonds : bond 0.05062 ( 1045) hydrogen bonds : angle 3.53253 ( 3069) metal coordination : bond 0.00340 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 411 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 MET cc_start: 0.8491 (mpp) cc_final: 0.8015 (mpp) REVERT: E 227 SER cc_start: 0.8651 (m) cc_final: 0.8366 (t) REVERT: E 239 GLU cc_start: 0.8395 (tp30) cc_final: 0.8065 (tp30) REVERT: E 254 SER cc_start: 0.8167 (t) cc_final: 0.7939 (t) REVERT: E 274 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7740 (tm-30) REVERT: E 309 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7696 (ttmm) REVERT: E 319 MET cc_start: 0.8476 (mtm) cc_final: 0.8246 (mtm) REVERT: E 330 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: A 65 ASP cc_start: 0.7587 (t0) cc_final: 0.7351 (t0) REVERT: A 83 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 90 MET cc_start: 0.6157 (mmp) cc_final: 0.5934 (mmp) REVERT: A 146 ASP cc_start: 0.5886 (m-30) cc_final: 0.5576 (p0) REVERT: A 191 TYR cc_start: 0.4744 (OUTLIER) cc_final: 0.4216 (t80) REVERT: A 196 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7188 (pmtt) REVERT: A 201 MET cc_start: 0.7372 (tmm) cc_final: 0.7100 (tmm) REVERT: A 248 LYS cc_start: 0.5606 (pmtt) cc_final: 0.4866 (tttp) REVERT: A 257 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: A 280 PHE cc_start: 0.7589 (m-10) cc_final: 0.7285 (m-10) REVERT: A 305 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 309 ASN cc_start: 0.8074 (m110) cc_final: 0.7453 (m110) REVERT: A 317 LYS cc_start: 0.7966 (tppt) cc_final: 0.7304 (tppt) REVERT: A 351 ASN cc_start: 0.8774 (m-40) cc_final: 0.8550 (m-40) REVERT: A 368 GLN cc_start: 0.8536 (mt0) cc_final: 0.8285 (mt0) REVERT: A 422 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7834 (mmtt) REVERT: A 447 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: C 10 ASN cc_start: 0.7801 (t0) cc_final: 0.7434 (m110) REVERT: C 54 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7980 (m90) REVERT: C 115 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7862 (mmtm) REVERT: C 123 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6888 (mt) REVERT: C 156 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7972 (mttt) REVERT: C 247 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7767 (mm-40) REVERT: C 292 MET cc_start: 0.7810 (mmt) cc_final: 0.7594 (mmt) REVERT: C 312 LYS cc_start: 0.8631 (mttt) cc_final: 0.8393 (mtpp) REVERT: C 313 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8172 (t) REVERT: C 328 LEU cc_start: 0.8415 (mt) cc_final: 0.8203 (mt) REVERT: C 395 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: D 155 TYR cc_start: 0.6456 (m-10) cc_final: 0.6252 (m-10) REVERT: D 198 ARG cc_start: 0.7683 (mtp85) cc_final: 0.6992 (ttp80) REVERT: D 248 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8309 (t) REVERT: D 253 GLU cc_start: 0.8233 (tp30) cc_final: 0.7801 (tp30) REVERT: D 286 MET cc_start: 0.8103 (mmm) cc_final: 0.7618 (mmm) REVERT: F 77 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7497 (tm-30) REVERT: F 144 GLU cc_start: 0.8410 (tt0) cc_final: 0.8078 (mt-10) REVERT: F 246 GLU cc_start: 0.7976 (tp30) cc_final: 0.7637 (tp30) REVERT: F 261 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8153 (t80) REVERT: F 308 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7895 (ttmm) REVERT: G 14 GLN cc_start: 0.7574 (mm110) cc_final: 0.7354 (mm110) REVERT: G 36 GLU cc_start: 0.7557 (tt0) cc_final: 0.6859 (tm-30) REVERT: G 74 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7668 (p) REVERT: G 147 GLN cc_start: 0.8140 (tp40) cc_final: 0.7738 (tt0) REVERT: G 165 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8436 (mmmt) REVERT: H 16 LEU cc_start: 0.7622 (tm) cc_final: 0.7387 (tt) REVERT: H 107 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: H 137 VAL cc_start: 0.7576 (m) cc_final: 0.7282 (t) REVERT: H 199 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7102 (mmm160) REVERT: P 55 ASP cc_start: 0.8104 (t70) cc_final: 0.7763 (t70) outliers start: 83 outliers final: 59 residues processed: 464 average time/residue: 0.7187 time to fit residues: 364.4889 Evaluate side-chains 484 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 409 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 134 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN B 436 GLN C 136 ASN C 147 GLN C 282 HIS D 206 GLN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN G 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114922 restraints weight = 24945.116| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.27 r_work: 0.3376 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17692 Z= 0.136 Angle : 0.533 8.019 23909 Z= 0.276 Chirality : 0.039 0.190 2719 Planarity : 0.004 0.058 3060 Dihedral : 4.952 59.030 2366 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.26 % Allowed : 26.14 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2147 helix: 2.01 (0.14), residues: 1456 sheet: -0.15 (0.42), residues: 167 loop : -1.93 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 207 TYR 0.015 0.001 TYR C 244 PHE 0.015 0.001 PHE E 96 TRP 0.033 0.001 TRP F 124 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00310 (17690) covalent geometry : angle 0.53350 (23909) hydrogen bonds : bond 0.05016 ( 1045) hydrogen bonds : angle 3.52354 ( 3069) metal coordination : bond 0.00329 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 409 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 MET cc_start: 0.8441 (mpp) cc_final: 0.7987 (mpp) REVERT: E 227 SER cc_start: 0.8645 (m) cc_final: 0.8356 (t) REVERT: E 239 GLU cc_start: 0.8372 (tp30) cc_final: 0.8022 (tp30) REVERT: E 254 SER cc_start: 0.8156 (t) cc_final: 0.7922 (t) REVERT: E 274 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7710 (tm-30) REVERT: E 309 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7673 (ttmm) REVERT: E 319 MET cc_start: 0.8454 (mtm) cc_final: 0.8218 (mtm) REVERT: E 330 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: A 65 ASP cc_start: 0.7577 (t0) cc_final: 0.7341 (t0) REVERT: A 90 MET cc_start: 0.6138 (mmp) cc_final: 0.5919 (mmp) REVERT: A 146 ASP cc_start: 0.5881 (m-30) cc_final: 0.5543 (p0) REVERT: A 191 TYR cc_start: 0.4664 (OUTLIER) cc_final: 0.4153 (t80) REVERT: A 196 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7189 (pmtt) REVERT: A 201 MET cc_start: 0.7364 (tmm) cc_final: 0.7085 (tmm) REVERT: A 257 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 280 PHE cc_start: 0.7587 (m-10) cc_final: 0.7217 (m-10) REVERT: A 305 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 309 ASN cc_start: 0.8026 (m110) cc_final: 0.7410 (m110) REVERT: A 317 LYS cc_start: 0.7926 (tppt) cc_final: 0.7273 (tppt) REVERT: A 351 ASN cc_start: 0.8701 (m-40) cc_final: 0.8474 (m-40) REVERT: A 368 GLN cc_start: 0.8521 (mt0) cc_final: 0.8263 (mt0) REVERT: A 422 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7809 (mmtt) REVERT: A 447 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: C 10 ASN cc_start: 0.7775 (t0) cc_final: 0.7409 (m110) REVERT: C 54 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7973 (m90) REVERT: C 115 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7847 (mmtm) REVERT: C 123 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6868 (mt) REVERT: C 235 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8557 (mp) REVERT: C 247 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7799 (mm-40) REVERT: C 292 MET cc_start: 0.7758 (mmt) cc_final: 0.7538 (mmt) REVERT: C 312 LYS cc_start: 0.8601 (mttt) cc_final: 0.8362 (mtpp) REVERT: C 313 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8159 (t) REVERT: C 328 LEU cc_start: 0.8400 (mt) cc_final: 0.8190 (mt) REVERT: C 395 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: D 198 ARG cc_start: 0.7654 (mtp85) cc_final: 0.6963 (ttp80) REVERT: D 248 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8265 (t) REVERT: D 253 GLU cc_start: 0.8252 (tp30) cc_final: 0.7768 (tp30) REVERT: D 256 GLN cc_start: 0.8504 (mt0) cc_final: 0.8180 (mt0) REVERT: D 286 MET cc_start: 0.8049 (mmm) cc_final: 0.7566 (mmm) REVERT: F 77 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7465 (tm-30) REVERT: F 96 GLU cc_start: 0.7354 (mp0) cc_final: 0.7131 (mp0) REVERT: F 144 GLU cc_start: 0.8391 (tt0) cc_final: 0.8051 (mt-10) REVERT: F 246 GLU cc_start: 0.7957 (tp30) cc_final: 0.7616 (tp30) REVERT: F 261 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (t80) REVERT: F 308 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7891 (ttmm) REVERT: G 14 GLN cc_start: 0.7535 (mm110) cc_final: 0.7312 (mm110) REVERT: G 36 GLU cc_start: 0.7538 (tt0) cc_final: 0.6847 (tm-30) REVERT: G 74 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7649 (p) REVERT: G 147 GLN cc_start: 0.8104 (tp40) cc_final: 0.7703 (tt0) REVERT: G 165 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8419 (mmmt) REVERT: H 16 LEU cc_start: 0.7587 (tm) cc_final: 0.7346 (tt) REVERT: H 107 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: H 137 VAL cc_start: 0.7510 (m) cc_final: 0.7239 (t) REVERT: H 199 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.7054 (mmm160) REVERT: P 55 ASP cc_start: 0.8131 (t70) cc_final: 0.7779 (t70) outliers start: 81 outliers final: 60 residues processed: 458 average time/residue: 0.7195 time to fit residues: 359.7327 Evaluate side-chains 485 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 410 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 395 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain P residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 431 GLN B 436 GLN C 136 ASN C 282 HIS D 206 GLN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN F 155 ASN G 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114080 restraints weight = 25251.553| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.30 r_work: 0.3364 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17692 Z= 0.155 Angle : 0.550 8.214 23909 Z= 0.283 Chirality : 0.039 0.151 2719 Planarity : 0.004 0.061 3060 Dihedral : 5.049 59.776 2366 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.26 % Allowed : 26.41 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2147 helix: 1.97 (0.14), residues: 1454 sheet: -0.24 (0.42), residues: 169 loop : -1.90 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 207 TYR 0.030 0.001 TYR D 155 PHE 0.016 0.001 PHE E 96 TRP 0.032 0.002 TRP F 124 HIS 0.008 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00365 (17690) covalent geometry : angle 0.55014 (23909) hydrogen bonds : bond 0.05321 ( 1045) hydrogen bonds : angle 3.56129 ( 3069) metal coordination : bond 0.00414 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7778.70 seconds wall clock time: 132 minutes 37.12 seconds (7957.12 seconds total)