Starting phenix.real_space_refine on Thu Feb 5 15:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5z_47532/02_2026/9e5z_47532_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5z_47532/02_2026/9e5z_47532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e5z_47532/02_2026/9e5z_47532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5z_47532/02_2026/9e5z_47532.map" model { file = "/net/cci-nas-00/data/ceres_data/9e5z_47532/02_2026/9e5z_47532_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5z_47532/02_2026/9e5z_47532_neut.cif" } resolution = 3.4 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= 0.000 sd= 0.067 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 104 5.16 5 C 11603 2.51 5 N 3124 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18279 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3284 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 9, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1687 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3216 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain: "D" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2477 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2362 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "F" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2182 Classifications: {'peptide': 272} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain breaks: 1 Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1383 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.17 Number of scatterers: 18279 At special positions: 0 Unit cell: (123.48, 142.8, 182.28, 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 104 16.00 O 3447 8.00 N 3124 7.00 C 11603 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: 1.55 Conformation dependent library (CDL) restraints added in 654.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 138 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 140 " 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 5 sheets defined 67.7% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.667A pdb=" N TYR A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.714A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.605A pdb=" N GLU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.841A pdb=" N GLU A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 155 removed outlier: 4.289A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.876A pdb=" N ASP A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.534A pdb=" N ARG A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 removed outlier: 4.281A pdb=" N VAL A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.551A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.837A pdb=" N ALA A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.567A pdb=" N LYS A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.979A 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 337 through 348 removed outlier: 3.566A pdb=" N LEU A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 358 through 378 removed outlier: 4.310A pdb=" N ARG A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.615A pdb=" N ASP A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 463 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.543A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 4.503A pdb=" N PHE B 259 " --> pdb=" O HIS B 255 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 287 removed outlier: 4.408A pdb=" N THR B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.791A pdb=" N ASP B 295 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 296' Processing helix chain 'B' and resid 309 through 321 removed outlier: 4.321A pdb=" N VAL B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 343 through 351 removed outlier: 4.832A pdb=" N GLU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.705A pdb=" N GLN B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.548A pdb=" N LYS B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 440 removed outlier: 3.590A pdb=" N SER B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.519A pdb=" N CYS C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) 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 47 removed outlier: 4.491A pdb=" N VAL C 45 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.523A pdb=" N GLY C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.931A pdb=" N ILE C 93 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.685A pdb=" N GLY C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 removed outlier: 4.396A pdb=" N GLY C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.604A pdb=" N ASP C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.967A pdb=" N GLN C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 150 " --> pdb=" O CYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.040A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.678A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 223 removed outlier: 3.501A pdb=" N SER C 223 " --> pdb=" O MET C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 223' Processing helix chain 'C' and resid 224 through 235 removed outlier: 3.589A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.553A pdb=" N LEU C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 295 through 310 removed outlier: 4.006A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.568A pdb=" N LYS C 336 " --> pdb=" O GLN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 399 removed outlier: 3.559A pdb=" N GLU C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 397 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.616A pdb=" N VAL C 404 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 405 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 116 removed outlier: 3.530A pdb=" N HIS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.546A pdb=" N ALA D 124 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.609A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.635A pdb=" N ARG D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.822A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 171 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.962A pdb=" N ILE D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.801A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 4.028A pdb=" N LYS D 266 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 removed outlier: 3.533A pdb=" N LEU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 298 through 312 Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.714A pdb=" N ALA D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 345 removed outlier: 3.574A pdb=" N GLU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 392 Processing helix chain 'D' and resid 392 through 401 removed outlier: 3.528A pdb=" N GLN D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.700A pdb=" N ILE E 28 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 44 through 47 Processing helix chain 'E' and resid 59 through 72 Processing helix chain 'E' and resid 109 through 112 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.789A pdb=" N PHE E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 215 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 242 Processing helix chain 'E' and resid 260 through 281 removed outlier: 3.630A pdb=" N GLY E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 329 removed outlier: 4.034A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 320 " --> pdb=" O HIS E 316 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.795A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 116 removed outlier: 3.880A pdb=" N GLN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 115 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.602A pdb=" N LYS F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 216 through 221 removed outlier: 3.512A pdb=" N HIS F 220 " --> pdb=" O THR F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 248 removed outlier: 3.721A pdb=" N ILE F 228 " --> pdb=" O GLN F 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 229 " --> pdb=" O HIS F 225 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG F 234 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.517A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 313 removed outlier: 5.200A pdb=" N TYR F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 60 through 73 removed outlier: 3.643A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 80 removed outlier: 3.676A pdb=" N ALA G 80 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.592A pdb=" N GLN G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.549A pdb=" N THR G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 220 removed outlier: 3.525A pdb=" N GLU G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 33 through 47 removed outlier: 3.679A pdb=" N LEU H 45 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS H 47 " --> pdb=" O LEU H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.680A pdb=" N TYR H 55 " --> pdb=" O ASN H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 77 through 83 Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.534A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 121 removed outlier: 4.926A pdb=" N ARG H 110 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 149 removed outlier: 3.566A pdb=" N LEU H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 169 through 182 Processing sheet with id=AA1, first strand: chain 'G' and resid 110 through 112 removed outlier: 5.213A pdb=" N LEU G 152 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP G 146 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL G 154 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS G 144 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.474A 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: 5.897A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA3, first strand: chain 'E' and resid 221 through 223 removed outlier: 8.502A pdb=" N VAL E 168 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA E 133 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY E 83 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS E 84 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE E 92 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP E 86 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N MET E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 11.659A pdb=" N PHE E 96 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.483A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TRP F 124 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY F 70 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU F 77 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 91 through 94 996 hydrogen bonds defined for protein. 2892 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: 2.22 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3101 1.31 - 1.43: 4723 1.43 - 1.56: 10616 1.56 - 1.69: 3 1.69 - 1.82: 167 Bond restraints: 18610 Sorted by residual: bond pdb=" CA CYS C 154 " pdb=" CB CYS C 154 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.13e-02 7.83e+03 3.56e+01 bond pdb=" CA CYS C 154 " pdb=" C CYS C 154 " ideal model delta sigma weight residual 1.532 1.462 0.071 1.21e-02 6.83e+03 3.43e+01 bond pdb=" CA ALA C 152 " pdb=" C ALA C 152 " ideal model delta sigma weight residual 1.531 1.460 0.072 1.46e-02 4.69e+03 2.41e+01 bond pdb=" CA GLU D 253 " pdb=" C GLU D 253 " ideal model delta sigma weight residual 1.520 1.460 0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" C LYS C 153 " pdb=" O LYS C 153 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.26e-02 6.30e+03 1.77e+01 ... (remaining 18605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 24801 2.47 - 4.94: 299 4.94 - 7.42: 32 7.42 - 9.89: 15 9.89 - 12.36: 6 Bond angle restraints: 25153 Sorted by residual: angle pdb=" N SER C 70 " pdb=" CA SER C 70 " pdb=" C SER C 70 " ideal model delta sigma weight residual 110.44 98.08 12.36 1.20e+00 6.94e-01 1.06e+02 angle pdb=" N GLU D 253 " pdb=" CA GLU D 253 " pdb=" C GLU D 253 " ideal model delta sigma weight residual 114.04 105.48 8.56 1.24e+00 6.50e-01 4.76e+01 angle pdb=" C SER D 297 " pdb=" N SER D 298 " pdb=" CA SER D 298 " ideal model delta sigma weight residual 120.71 111.12 9.59 1.42e+00 4.96e-01 4.56e+01 angle pdb=" C PHE C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 120.38 111.94 8.44 1.37e+00 5.33e-01 3.80e+01 angle pdb=" N VAL C 404 " pdb=" CA VAL C 404 " pdb=" C VAL C 404 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.77e+01 ... (remaining 25148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9461 17.97 - 35.94: 1410 35.94 - 53.91: 392 53.91 - 71.88: 63 71.88 - 89.85: 34 Dihedral angle restraints: 11360 sinusoidal: 4616 harmonic: 6744 Sorted by residual: dihedral pdb=" CA CYS A 251 " pdb=" C CYS A 251 " pdb=" N ALA A 252 " pdb=" CA ALA A 252 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP A 65 " pdb=" C ASP A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LEU A 70 " pdb=" C LEU A 70 " pdb=" N ARG A 71 " pdb=" CA ARG A 71 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 11357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2557 0.064 - 0.128: 278 0.128 - 0.192: 8 0.192 - 0.255: 1 0.255 - 0.319: 2 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CA PHE C 74 " pdb=" N PHE C 74 " pdb=" C PHE C 74 " pdb=" CB PHE C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB VAL C 64 " pdb=" CA VAL C 64 " pdb=" CG1 VAL C 64 " pdb=" CG2 VAL C 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA LYS C 153 " pdb=" N LYS C 153 " pdb=" C LYS C 153 " pdb=" CB LYS C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2843 not shown) Planarity restraints: 3230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 292 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO B 293 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO B 293 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 293 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 43 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO E 44 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 156 " 0.051 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO C 157 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.042 5.00e-02 4.00e+02 ... (remaining 3227 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 128 2.55 - 3.14: 14268 3.14 - 3.73: 27810 3.73 - 4.31: 37422 4.31 - 4.90: 63403 Nonbonded interactions: 143031 Sorted by model distance: nonbonded pdb=" OE1 GLU E 104 " pdb="ZN ZN E 401 " model vdw 1.966 2.230 nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 401 " model vdw 1.967 2.230 nonbonded pdb=" OE2 GLU E 104 " pdb="ZN ZN E 401 " model vdw 2.084 2.230 nonbonded pdb=" OD1 ASN C 271 " pdb=" OG SER C 273 " model vdw 2.198 3.040 nonbonded pdb=" CD GLU E 104 " pdb="ZN ZN E 401 " model vdw 2.209 2.460 ... (remaining 143026 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: 4.370 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.004 0.104 18612 Z= 0.231 Angle : 0.708 12.362 25153 Z= 0.401 Chirality : 0.041 0.319 2846 Planarity : 0.005 0.114 3230 Dihedral : 18.547 89.851 6986 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.59 % Favored : 92.75 % Rotamer: Outliers : 0.65 % Allowed : 27.81 % Favored : 71.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.90 % 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: -0.38 (0.18), residues: 2261 helix: 0.72 (0.15), residues: 1405 sheet: -0.79 (0.43), residues: 151 loop : -2.08 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 135 TYR 0.019 0.001 TYR A 357 PHE 0.020 0.001 PHE C 84 TRP 0.014 0.001 TRP A 130 HIS 0.012 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00441 (18610) covalent geometry : angle 0.70790 (25153) hydrogen bonds : bond 0.17384 ( 996) hydrogen bonds : angle 5.91544 ( 2892) metal coordination : bond 0.00490 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.618 Fit side-chains REVERT: A 211 TYR cc_start: 0.7766 (m-80) cc_final: 0.7375 (m-80) REVERT: B 238 ARG cc_start: 0.6453 (mmt180) cc_final: 0.4770 (tpt170) REVERT: C 21 MET cc_start: 0.8402 (mmt) cc_final: 0.8038 (mmt) REVERT: C 91 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7078 (tm-30) REVERT: D 196 ASP cc_start: 0.8449 (t0) cc_final: 0.8172 (t0) outliers start: 13 outliers final: 6 residues processed: 194 average time/residue: 0.1362 time to fit residues: 39.9522 Evaluate side-chains 169 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain F residue 250 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 0.0060 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN F 310 ASN G 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097047 restraints weight = 32245.566| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.33 r_work: 0.3111 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18612 Z= 0.118 Angle : 0.557 8.742 25153 Z= 0.288 Chirality : 0.039 0.188 2846 Planarity : 0.005 0.089 3230 Dihedral : 4.523 32.358 2484 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.10 % Rotamer: Outliers : 2.10 % Allowed : 25.36 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.15 (0.19), residues: 2261 helix: 1.10 (0.15), residues: 1441 sheet: -0.69 (0.42), residues: 151 loop : -1.93 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 170 TYR 0.021 0.001 TYR E 114 PHE 0.020 0.001 PHE B 262 TRP 0.007 0.001 TRP H 82 HIS 0.010 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00257 (18610) covalent geometry : angle 0.55679 (25153) hydrogen bonds : bond 0.04267 ( 996) hydrogen bonds : angle 4.25280 ( 2892) metal coordination : bond 0.00397 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 211 TYR cc_start: 0.7777 (m-80) cc_final: 0.7358 (m-80) REVERT: B 238 ARG cc_start: 0.6368 (mmt180) cc_final: 0.4570 (tpt170) REVERT: B 255 HIS cc_start: 0.3242 (OUTLIER) cc_final: 0.1579 (t-90) REVERT: D 196 ASP cc_start: 0.8483 (t0) cc_final: 0.8211 (t0) REVERT: E 194 LYS cc_start: 0.9075 (tppt) cc_final: 0.8663 (tptp) REVERT: H 118 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7508 (t80) outliers start: 42 outliers final: 13 residues processed: 213 average time/residue: 0.1298 time to fit residues: 41.8937 Evaluate side-chains 179 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 118 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN F 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093453 restraints weight = 32459.795| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.35 r_work: 0.3042 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18612 Z= 0.167 Angle : 0.568 11.060 25153 Z= 0.289 Chirality : 0.040 0.182 2846 Planarity : 0.004 0.090 3230 Dihedral : 4.415 29.857 2476 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.86 % Favored : 92.92 % Rotamer: Outliers : 2.80 % Allowed : 24.86 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.15 (0.18), residues: 2261 helix: 1.13 (0.15), residues: 1442 sheet: -0.89 (0.42), residues: 146 loop : -1.92 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 258 TYR 0.016 0.001 TYR C 267 PHE 0.012 0.001 PHE E 96 TRP 0.007 0.001 TRP D 370 HIS 0.010 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00401 (18610) covalent geometry : angle 0.56801 (25153) hydrogen bonds : bond 0.04300 ( 996) hydrogen bonds : angle 4.09439 ( 2892) metal coordination : bond 0.00644 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 238 ARG cc_start: 0.6505 (mmt180) cc_final: 0.4772 (tpt170) REVERT: B 255 HIS cc_start: 0.3264 (OUTLIER) cc_final: 0.1644 (t-90) REVERT: B 430 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8367 (mm-40) REVERT: C 15 LEU cc_start: 0.8962 (tp) cc_final: 0.8753 (tt) REVERT: C 159 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9209 (mm) REVERT: D 196 ASP cc_start: 0.8474 (t0) cc_final: 0.8200 (t0) REVERT: E 194 LYS cc_start: 0.9078 (tppt) cc_final: 0.8764 (tptp) REVERT: E 282 ARG cc_start: 0.6584 (ttp-110) cc_final: 0.6247 (mtp180) REVERT: F 75 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8615 (mtmm) REVERT: G 179 ASP cc_start: 0.8432 (m-30) cc_final: 0.8170 (m-30) REVERT: H 43 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8651 (tt) REVERT: H 118 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7508 (t80) outliers start: 56 outliers final: 23 residues processed: 226 average time/residue: 0.1334 time to fit residues: 45.6327 Evaluate side-chains 198 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093215 restraints weight = 31741.344| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.47 r_work: 0.3014 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18612 Z= 0.175 Angle : 0.566 10.011 25153 Z= 0.288 Chirality : 0.040 0.155 2846 Planarity : 0.004 0.090 3230 Dihedral : 4.439 29.889 2476 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.03 % Favored : 92.75 % Rotamer: Outliers : 3.05 % Allowed : 25.26 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.15 (0.18), residues: 2261 helix: 1.15 (0.15), residues: 1441 sheet: -1.00 (0.41), residues: 146 loop : -1.94 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 344 TYR 0.015 0.001 TYR C 267 PHE 0.025 0.001 PHE C 8 TRP 0.007 0.001 TRP A 130 HIS 0.012 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00423 (18610) covalent geometry : angle 0.56580 (25153) hydrogen bonds : bond 0.04216 ( 996) hydrogen bonds : angle 4.04817 ( 2892) metal coordination : bond 0.00641 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: B 238 ARG cc_start: 0.6608 (mmt180) cc_final: 0.4671 (tpt170) REVERT: B 255 HIS cc_start: 0.3354 (OUTLIER) cc_final: 0.1540 (t-90) REVERT: B 430 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8520 (mm-40) REVERT: C 15 LEU cc_start: 0.8973 (tp) cc_final: 0.8759 (tt) REVERT: C 114 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8186 (ttm170) REVERT: C 159 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9237 (mm) REVERT: D 196 ASP cc_start: 0.8493 (t0) cc_final: 0.8215 (t0) REVERT: D 245 MET cc_start: 0.9414 (tpt) cc_final: 0.8966 (tpt) REVERT: E 65 MET cc_start: 0.9274 (mtt) cc_final: 0.8999 (mtt) REVERT: E 125 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8369 (mmtm) REVERT: E 194 LYS cc_start: 0.9023 (tppt) cc_final: 0.8768 (tptp) REVERT: G 179 ASP cc_start: 0.8489 (m-30) cc_final: 0.8234 (m-30) REVERT: H 43 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8686 (tt) REVERT: H 118 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7486 (t80) outliers start: 61 outliers final: 34 residues processed: 223 average time/residue: 0.1298 time to fit residues: 44.5932 Evaluate side-chains 214 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 chunk 195 optimal weight: 3.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.127043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094397 restraints weight = 31465.691| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.48 r_work: 0.3042 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18612 Z= 0.128 Angle : 0.542 11.115 25153 Z= 0.275 Chirality : 0.039 0.273 2846 Planarity : 0.004 0.089 3230 Dihedral : 4.351 29.615 2475 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 2.95 % Allowed : 25.06 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.27 (0.19), residues: 2261 helix: 1.24 (0.15), residues: 1442 sheet: -0.92 (0.41), residues: 146 loop : -1.90 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 204 TYR 0.015 0.001 TYR A 357 PHE 0.028 0.001 PHE C 8 TRP 0.007 0.001 TRP A 130 HIS 0.007 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00298 (18610) covalent geometry : angle 0.54179 (25153) hydrogen bonds : bond 0.03833 ( 996) hydrogen bonds : angle 3.94715 ( 2892) metal coordination : bond 0.00454 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8251 (pp30) REVERT: A 172 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: B 238 ARG cc_start: 0.6586 (mmt180) cc_final: 0.4343 (tpt-90) REVERT: B 255 HIS cc_start: 0.3280 (OUTLIER) cc_final: 0.1594 (t-90) REVERT: B 430 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8572 (mm-40) REVERT: C 15 LEU cc_start: 0.8964 (tp) cc_final: 0.8740 (tt) REVERT: C 159 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9214 (mm) REVERT: D 153 ARG cc_start: 0.7939 (ptp90) cc_final: 0.7625 (ptp-170) REVERT: D 196 ASP cc_start: 0.8451 (t0) cc_final: 0.8166 (t0) REVERT: E 125 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8336 (mmtm) REVERT: E 194 LYS cc_start: 0.8988 (tppt) cc_final: 0.8769 (tptp) REVERT: F 75 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8606 (mtmm) REVERT: H 43 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8668 (tt) REVERT: H 59 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8425 (ptt180) REVERT: H 118 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7505 (t80) outliers start: 59 outliers final: 32 residues processed: 228 average time/residue: 0.1322 time to fit residues: 45.6649 Evaluate side-chains 212 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 145 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 193 optimal weight: 0.0270 chunk 208 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094796 restraints weight = 32108.557| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.41 r_work: 0.3074 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18612 Z= 0.105 Angle : 0.525 11.651 25153 Z= 0.268 Chirality : 0.038 0.219 2846 Planarity : 0.004 0.089 3230 Dihedral : 4.264 29.508 2475 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Rotamer: Outliers : 2.50 % Allowed : 25.66 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.44 (0.19), residues: 2261 helix: 1.38 (0.15), residues: 1435 sheet: -0.83 (0.41), residues: 146 loop : -1.83 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 205 TYR 0.014 0.001 TYR A 357 PHE 0.029 0.001 PHE C 8 TRP 0.007 0.001 TRP A 130 HIS 0.012 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00233 (18610) covalent geometry : angle 0.52500 (25153) hydrogen bonds : bond 0.03421 ( 996) hydrogen bonds : angle 3.80282 ( 2892) metal coordination : bond 0.00315 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8182 (pp30) REVERT: B 238 ARG cc_start: 0.6592 (mmt180) cc_final: 0.4323 (mmt180) REVERT: B 255 HIS cc_start: 0.3158 (OUTLIER) cc_final: 0.1617 (t-90) REVERT: B 430 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8530 (mm-40) REVERT: C 15 LEU cc_start: 0.8940 (tp) cc_final: 0.8729 (tt) REVERT: C 159 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9182 (mm) REVERT: D 153 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7627 (ptp-170) REVERT: D 196 ASP cc_start: 0.8412 (t0) cc_final: 0.8205 (t0) REVERT: E 125 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8305 (mmtm) REVERT: F 75 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (mtmm) REVERT: H 43 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8616 (tt) REVERT: H 59 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8325 (ptt180) REVERT: H 118 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7484 (t80) outliers start: 50 outliers final: 29 residues processed: 229 average time/residue: 0.1247 time to fit residues: 43.4894 Evaluate side-chains 211 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 170 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091972 restraints weight = 31710.827| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.26 r_work: 0.3044 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18612 Z= 0.180 Angle : 0.591 11.469 25153 Z= 0.294 Chirality : 0.040 0.165 2846 Planarity : 0.004 0.088 3230 Dihedral : 4.350 30.855 2475 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Rotamer: Outliers : 3.00 % Allowed : 25.46 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.30 (0.18), residues: 2261 helix: 1.27 (0.15), residues: 1438 sheet: -0.95 (0.41), residues: 146 loop : -1.88 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 205 TYR 0.017 0.001 TYR C 267 PHE 0.012 0.001 PHE E 96 TRP 0.009 0.001 TRP A 130 HIS 0.012 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00436 (18610) covalent geometry : angle 0.59081 (25153) hydrogen bonds : bond 0.04043 ( 996) hydrogen bonds : angle 3.90001 ( 2892) metal coordination : bond 0.00634 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8147 (pp30) REVERT: B 238 ARG cc_start: 0.6589 (mmt180) cc_final: 0.4329 (mmt180) REVERT: B 255 HIS cc_start: 0.3311 (OUTLIER) cc_final: 0.1425 (t-90) REVERT: B 430 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8610 (mm-40) REVERT: D 153 ARG cc_start: 0.7985 (ptp90) cc_final: 0.7648 (ptp-170) REVERT: D 196 ASP cc_start: 0.8418 (t0) cc_final: 0.8198 (t0) REVERT: D 245 MET cc_start: 0.9371 (tpt) cc_final: 0.8969 (tpt) REVERT: E 65 MET cc_start: 0.9275 (mtm) cc_final: 0.8989 (mtt) REVERT: E 194 LYS cc_start: 0.8985 (tptt) cc_final: 0.8764 (tppt) REVERT: F 75 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8599 (mtmm) REVERT: H 43 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8657 (tt) outliers start: 60 outliers final: 40 residues processed: 227 average time/residue: 0.1303 time to fit residues: 45.2118 Evaluate side-chains 217 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS D 169 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093421 restraints weight = 32261.113| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.46 r_work: 0.3040 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18612 Z= 0.127 Angle : 0.569 10.659 25153 Z= 0.282 Chirality : 0.039 0.150 2846 Planarity : 0.004 0.086 3230 Dihedral : 4.320 31.464 2475 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.88 % Rotamer: Outliers : 2.80 % Allowed : 25.96 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.38 (0.19), residues: 2261 helix: 1.36 (0.15), residues: 1436 sheet: -0.99 (0.41), residues: 146 loop : -1.89 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 205 TYR 0.017 0.001 TYR A 357 PHE 0.017 0.001 PHE C 8 TRP 0.007 0.001 TRP A 130 HIS 0.012 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00297 (18610) covalent geometry : angle 0.56899 (25153) hydrogen bonds : bond 0.03660 ( 996) hydrogen bonds : angle 3.85133 ( 2892) metal coordination : bond 0.00443 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8155 (pp30) REVERT: B 238 ARG cc_start: 0.6520 (mmt180) cc_final: 0.4237 (mmt180) REVERT: B 255 HIS cc_start: 0.3234 (OUTLIER) cc_final: 0.1403 (t-90) REVERT: B 430 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8646 (mm-40) REVERT: C 151 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (mp) REVERT: D 153 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7518 (ptp-170) REVERT: D 245 MET cc_start: 0.9365 (tpt) cc_final: 0.8970 (tpt) REVERT: D 295 ASP cc_start: 0.7490 (p0) cc_final: 0.7093 (p0) REVERT: E 65 MET cc_start: 0.9281 (mtm) cc_final: 0.8971 (mtt) REVERT: E 194 LYS cc_start: 0.9026 (tptt) cc_final: 0.8762 (tppt) REVERT: F 75 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8570 (mtmm) REVERT: F 101 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: H 43 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8650 (tt) REVERT: H 59 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (ptt180) outliers start: 56 outliers final: 39 residues processed: 224 average time/residue: 0.1279 time to fit residues: 43.7953 Evaluate side-chains 216 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 116 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.128046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093451 restraints weight = 32269.170| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.35 r_work: 0.3043 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18612 Z= 0.142 Angle : 0.579 10.925 25153 Z= 0.287 Chirality : 0.039 0.140 2846 Planarity : 0.004 0.086 3230 Dihedral : 4.310 32.553 2475 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.77 % Favored : 93.06 % Rotamer: Outliers : 2.65 % Allowed : 26.16 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.39 (0.19), residues: 2261 helix: 1.36 (0.15), residues: 1437 sheet: -0.98 (0.41), residues: 146 loop : -1.87 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 204 TYR 0.047 0.001 TYR A 357 PHE 0.013 0.001 PHE C 8 TRP 0.008 0.001 TRP A 130 HIS 0.023 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00339 (18610) covalent geometry : angle 0.57900 (25153) hydrogen bonds : bond 0.03725 ( 996) hydrogen bonds : angle 3.87070 ( 2892) metal coordination : bond 0.00510 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8132 (pp30) REVERT: A 453 MET cc_start: 0.9092 (tmm) cc_final: 0.8829 (ttp) REVERT: B 238 ARG cc_start: 0.6507 (mmt180) cc_final: 0.4241 (mmt180) REVERT: B 255 HIS cc_start: 0.3252 (OUTLIER) cc_final: 0.1411 (t-90) REVERT: B 430 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8609 (mm-40) REVERT: C 151 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8708 (mp) REVERT: D 153 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7549 (ptp-170) REVERT: D 245 MET cc_start: 0.9367 (tpt) cc_final: 0.8960 (tpt) REVERT: D 295 ASP cc_start: 0.7478 (p0) cc_final: 0.7098 (p0) REVERT: E 194 LYS cc_start: 0.9013 (tptt) cc_final: 0.8756 (tppt) REVERT: F 75 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8585 (mtmm) REVERT: F 101 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: H 43 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8674 (tt) REVERT: H 59 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8410 (ptt180) outliers start: 53 outliers final: 39 residues processed: 219 average time/residue: 0.1328 time to fit residues: 44.1744 Evaluate side-chains 217 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 205 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 17 optimal weight: 0.0270 chunk 42 optimal weight: 0.0270 chunk 219 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095321 restraints weight = 32196.115| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.41 r_work: 0.3080 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18612 Z= 0.104 Angle : 0.557 11.360 25153 Z= 0.277 Chirality : 0.039 0.230 2846 Planarity : 0.004 0.088 3230 Dihedral : 4.231 32.247 2475 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.81 % Favored : 93.01 % Rotamer: Outliers : 1.90 % Allowed : 26.96 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.51 (0.19), residues: 2261 helix: 1.46 (0.15), residues: 1439 sheet: -0.89 (0.41), residues: 146 loop : -1.86 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 205 TYR 0.036 0.001 TYR A 357 PHE 0.012 0.001 PHE C 8 TRP 0.008 0.001 TRP H 57 HIS 0.035 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00226 (18610) covalent geometry : angle 0.55653 (25153) hydrogen bonds : bond 0.03260 ( 996) hydrogen bonds : angle 3.76531 ( 2892) metal coordination : bond 0.00248 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4522 Ramachandran restraints generated. 2261 Oldfield, 0 Emsley, 2261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 ARG cc_start: 0.6557 (mmt180) cc_final: 0.4271 (mmt180) REVERT: B 255 HIS cc_start: 0.3160 (OUTLIER) cc_final: 0.1393 (t-90) REVERT: B 430 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8619 (mm-40) REVERT: D 153 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7602 (ptp-170) REVERT: D 245 MET cc_start: 0.9341 (tpt) cc_final: 0.8931 (tpt) REVERT: D 295 ASP cc_start: 0.7364 (p0) cc_final: 0.7118 (p0) REVERT: E 65 MET cc_start: 0.9298 (mtt) cc_final: 0.8964 (mtt) REVERT: E 81 MET cc_start: 0.8985 (ptm) cc_final: 0.8570 (ptm) REVERT: F 101 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: H 43 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8609 (tt) REVERT: H 59 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8316 (ptt180) outliers start: 38 outliers final: 29 residues processed: 210 average time/residue: 0.1305 time to fit residues: 41.9138 Evaluate side-chains 203 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 125 optimal weight: 0.0870 chunk 136 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 131 optimal weight: 0.1980 chunk 167 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 57 optimal weight: 0.0170 chunk 56 optimal weight: 0.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098274 restraints weight = 31514.584| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.37 r_work: 0.3117 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18612 Z= 0.098 Angle : 0.549 11.597 25153 Z= 0.272 Chirality : 0.038 0.196 2846 Planarity : 0.004 0.088 3230 Dihedral : 4.136 32.118 2475 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 1.85 % Allowed : 26.96 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.62 (0.19), residues: 2261 helix: 1.56 (0.15), residues: 1438 sheet: -0.78 (0.41), residues: 146 loop : -1.85 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 205 TYR 0.033 0.001 TYR A 357 PHE 0.020 0.001 PHE C 84 TRP 0.008 0.001 TRP H 57 HIS 0.008 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00214 (18610) covalent geometry : angle 0.54862 (25153) hydrogen bonds : bond 0.03045 ( 996) hydrogen bonds : angle 3.67170 ( 2892) metal coordination : bond 0.00181 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.55 seconds wall clock time: 78 minutes 37.77 seconds (4717.77 seconds total)