Starting phenix.real_space_refine on Fri Feb 6 15:03:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egl_47990/02_2026/9egl_47990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egl_47990/02_2026/9egl_47990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9egl_47990/02_2026/9egl_47990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egl_47990/02_2026/9egl_47990.map" model { file = "/net/cci-nas-00/data/ceres_data/9egl_47990/02_2026/9egl_47990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egl_47990/02_2026/9egl_47990.cif" } resolution = 3.93 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= 0.002 sd= 0.015 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 3 6.06 5 S 146 5.16 5 C 16115 2.51 5 N 4369 2.21 5 O 4760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 25393 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3271 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 8, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3342 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3222 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain: "D" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3241 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 9, 'TRANS': 395} Chain: "E" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2309 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 8, 'TRANS': 282} Chain breaks: 2 Chain: "F" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2201 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3451 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 413} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 693 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain breaks: 1 Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24903 SG CYS K 42 84.444 70.231 73.751 1.00152.90 S ATOM 24922 SG CYS K 45 86.132 67.439 75.799 1.00156.70 S ATOM 25179 SG CYS K 83 83.133 69.333 77.259 1.00156.88 S ATOM 25108 SG CYS K 75 81.626 80.761 67.041 1.00150.36 S ATOM 25275 SG CYS K 94 83.260 80.126 70.554 1.00130.19 S ATOM 24989 SG CYS K 53 80.865 65.607 78.215 1.00207.58 S ATOM 25012 SG CYS K 56 78.300 62.976 79.285 1.00220.50 S ATOM 25058 SG CYS K 68 78.682 64.010 75.438 1.00232.82 S Time building chain proxies: 5.92, per 1000 atoms: 0.23 Number of scatterers: 25393 At special positions: 0 Unit cell: (138.06, 167.265, 201.78, 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 3 29.99 S 146 16.00 O 4760 8.00 N 4369 7.00 C 16115 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 80 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 83 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 45 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 42 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 94 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 77 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 75 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 56 " Number of angles added : 6 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6054 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 10 sheets defined 67.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.504A pdb=" N TYR A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.887A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.935A pdb=" N ALA A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.534A pdb=" N GLU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 156 removed outlier: 3.557A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 194 through 213 Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.770A pdb=" N ASP A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.082A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.940A pdb=" N LEU A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 323 removed outlier: 4.144A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.514A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 removed outlier: 4.265A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 379 Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.814A pdb=" N LEU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 463 removed outlier: 3.587A pdb=" N LEU A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.684A pdb=" N LYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 124 through 142 Processing helix chain 'B' and resid 147 through 162 Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.880A pdb=" N LYS B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 3.796A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.799A pdb=" N ILE B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.695A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 removed outlier: 3.846A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 292 through 300 removed outlier: 5.196A pdb=" N GLN B 297 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 319 removed outlier: 4.208A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N MET B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.633A pdb=" N ASN B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.642A pdb=" N ILE B 347 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.533A pdb=" N LYS B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.549A 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 418 through 440 removed outlier: 3.652A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.690A pdb=" N GLY C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.763A pdb=" N CYS C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.694A pdb=" N LEU C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 removed outlier: 3.844A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 68 removed outlier: 3.824A pdb=" N MET C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 removed outlier: 4.146A pdb=" N LEU C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 96 through 114 removed outlier: 4.260A pdb=" N ARG C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 120 through 132 removed outlier: 4.469A pdb=" N ASP C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 153 removed outlier: 4.151A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 159 through 164 removed outlier: 4.183A pdb=" N VAL C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.606A pdb=" N TYR C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 217 through 235 removed outlier: 4.125A pdb=" N LEU C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 222 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.623A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 268 removed outlier: 4.025A pdb=" N HIS C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.684A pdb=" N ASN C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.655A pdb=" N PHE C 286 " --> pdb=" O HIS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 removed outlier: 3.763A pdb=" N LEU C 302 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 330 through 345 Processing helix chain 'C' and resid 369 through 398 removed outlier: 3.676A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 14 removed outlier: 4.422A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 removed outlier: 4.343A pdb=" N GLY D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 Processing helix chain 'D' and resid 58 through 72 removed outlier: 4.005A pdb=" N HIS D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.524A pdb=" N GLU D 100 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.956A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.524A pdb=" N ASP D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.550A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 201 through 212 Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.503A pdb=" N ASP D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 4.209A pdb=" N GLN D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 258' Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.771A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 284 removed outlier: 3.513A pdb=" N MET D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 328 removed outlier: 4.381A pdb=" N ALA D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 removed outlier: 3.862A pdb=" N GLU D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 392 removed outlier: 3.508A pdb=" N ALA D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'E' and resid 25 through 30 removed outlier: 4.073A pdb=" N ILE E 28 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS E 30 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 44 through 47 removed outlier: 3.733A pdb=" N LYS E 47 " --> pdb=" O PRO E 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 44 through 47' Processing helix chain 'E' and resid 59 through 72 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 128 removed outlier: 4.055A pdb=" N GLN E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 4.157A pdb=" N PHE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 258 through 281 removed outlier: 3.846A pdb=" N SER E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 329 removed outlier: 3.536A pdb=" N THR E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 63 Processing helix chain 'F' and resid 101 through 116 removed outlier: 4.222A pdb=" N GLN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL F 115 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.642A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 215 through 248 removed outlier: 3.990A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.657A pdb=" N GLU F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 removed outlier: 4.017A pdb=" N GLY F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 297 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.514A pdb=" N GLU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 48 removed outlier: 4.198A pdb=" N LEU G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 43 through 48' Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.810A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.637A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.719A pdb=" N THR G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 221 removed outlier: 3.611A pdb=" N LYS G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.574A pdb=" N ASN H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 removed outlier: 4.101A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.702A pdb=" N MET H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU H 107 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 152 removed outlier: 3.692A pdb=" N ALA H 144 " --> pdb=" O PRO H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 209 removed outlier: 3.583A pdb=" N ASN H 209 " --> pdb=" O ALA H 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 34 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'J' and resid 310 through 330 removed outlier: 4.354A pdb=" N SER J 330 " --> pdb=" O LYS J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 359 removed outlier: 3.525A pdb=" N SER J 359 " --> pdb=" O PHE J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 379 removed outlier: 4.108A pdb=" N ASN J 379 " --> pdb=" O GLU J 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 398 removed outlier: 3.654A pdb=" N LYS J 398 " --> pdb=" O ASP J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 421 removed outlier: 3.664A pdb=" N VAL J 408 " --> pdb=" O THR J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 438 removed outlier: 3.994A pdb=" N PHE J 428 " --> pdb=" O GLU J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 463 removed outlier: 3.970A pdb=" N GLU J 461 " --> pdb=" O LYS J 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 494 Processing helix chain 'J' and resid 496 through 501 removed outlier: 3.931A pdb=" N VAL J 501 " --> pdb=" O LEU J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 525 through 541 Processing helix chain 'J' and resid 596 through 608 removed outlier: 3.938A pdb=" N ASN J 607 " --> pdb=" O MET J 603 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG J 608 " --> pdb=" O LEU J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 613 through 619 removed outlier: 3.928A pdb=" N GLU J 619 " --> pdb=" O GLU J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 626 through 632 removed outlier: 3.755A pdb=" N ALA J 630 " --> pdb=" O GLU J 626 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 680 Processing helix chain 'J' and resid 695 through 713 Processing helix chain 'J' and resid 720 through 730 removed outlier: 3.581A pdb=" N THR J 727 " --> pdb=" O VAL J 723 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU J 730 " --> pdb=" O VAL J 726 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 748 removed outlier: 3.935A pdb=" N ILE J 741 " --> pdb=" O SER J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 749 through 751 No H-bonds generated for 'chain 'J' and resid 749 through 751' Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.342A pdb=" N THR K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 352 through 353 removed outlier: 7.409A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 369 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 358 through 360 removed outlier: 6.732A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP G 146 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 151 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 54 through 58 removed outlier: 6.982A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY E 135 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY E 83 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA E 133 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL E 168 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE E 229 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE E 57 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 40 through 43 removed outlier: 6.835A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET F 84 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 70 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 125 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY F 123 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY F 74 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE F 121 " --> pdb=" O GLY F 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'I' and resid 12 through 15 removed outlier: 6.725A pdb=" N LYS I 4 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU I 69 " --> pdb=" O LYS I 4 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N LEU I 71 " --> pdb=" O LYS I 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 508 through 509 removed outlier: 7.388A pdb=" N LEU J 508 " --> pdb=" O TRP K 33 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N TRP K 35 " --> pdb=" O LEU J 508 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA K 34 " --> pdb=" O GLN J 547 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN J 547 " --> pdb=" O ALA K 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 557 through 561 Processing sheet with id=AA9, first strand: chain 'J' and resid 611 through 612 removed outlier: 3.512A pdb=" N TYR J 611 " --> pdb=" O PHE J 659 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 70 through 71 1484 hydrogen bonds defined for protein. 4347 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: 4.94 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8132 1.34 - 1.46: 3864 1.46 - 1.58: 13606 1.58 - 1.70: 0 1.70 - 1.82: 235 Bond restraints: 25837 Sorted by residual: bond pdb=" CG GLN H 151 " pdb=" CD GLN H 151 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.42e+00 bond pdb=" N GLU I 28 " pdb=" CA GLU I 28 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.20e-02 6.94e+03 1.39e+00 bond pdb=" N THR J 765 " pdb=" CA THR J 765 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.15e-02 7.56e+03 1.32e+00 bond pdb=" C GLU J 647 " pdb=" N PRO J 648 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.17e+00 bond pdb=" CB LYS B 415 " pdb=" CG LYS B 415 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 25832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 34070 1.74 - 3.47: 628 3.47 - 5.21: 116 5.21 - 6.94: 34 6.94 - 8.68: 11 Bond angle restraints: 34859 Sorted by residual: angle pdb=" C CYS K 53 " pdb=" N ILE K 54 " pdb=" CA ILE K 54 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" CA LYS B 415 " pdb=" CB LYS B 415 " pdb=" CG LYS B 415 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" N GLU H 150 " pdb=" CA GLU H 150 " pdb=" CB GLU H 150 " ideal model delta sigma weight residual 110.07 115.27 -5.20 1.45e+00 4.76e-01 1.28e+01 angle pdb=" C CYS J 464 " pdb=" N GLN J 465 " pdb=" CA GLN J 465 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" CA LYS C 115 " pdb=" CB LYS C 115 " pdb=" CG LYS C 115 " ideal model delta sigma weight residual 114.10 120.80 -6.70 2.00e+00 2.50e-01 1.12e+01 ... (remaining 34854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 13946 17.59 - 35.18: 1502 35.18 - 52.78: 282 52.78 - 70.37: 46 70.37 - 87.96: 38 Dihedral angle restraints: 15814 sinusoidal: 6493 harmonic: 9321 Sorted by residual: dihedral pdb=" CA LYS C 115 " pdb=" C LYS C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta harmonic sigma weight residual 180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA TYR I 59 " pdb=" C TYR I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta harmonic sigma weight residual 180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY F 293 " pdb=" C GLY F 293 " pdb=" N THR F 294 " pdb=" CA THR F 294 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 15811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2639 0.034 - 0.068: 915 0.068 - 0.101: 288 0.101 - 0.135: 76 0.135 - 0.169: 13 Chirality restraints: 3931 Sorted by residual: chirality pdb=" CB ILE I 3 " pdb=" CA ILE I 3 " pdb=" CG1 ILE I 3 " pdb=" CG2 ILE I 3 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA GLN J 465 " pdb=" N GLN J 465 " pdb=" C GLN J 465 " pdb=" CB GLN J 465 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA GLU H 150 " pdb=" N GLU H 150 " pdb=" C GLU H 150 " pdb=" CB GLU H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 3928 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 116 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO C 117 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 315 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C LEU D 315 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU D 315 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR D 316 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 270 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 271 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " 0.034 5.00e-02 4.00e+02 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 18 2.57 - 3.15: 21112 3.15 - 3.73: 40580 3.73 - 4.32: 50828 4.32 - 4.90: 83684 Nonbonded interactions: 196222 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb="ZN ZN K 202 " model vdw 1.986 2.230 nonbonded pdb=" OD1 ASP K 97 " pdb="ZN ZN K 202 " model vdw 2.003 2.230 nonbonded pdb=" CG ASP K 97 " pdb="ZN ZN K 202 " model vdw 2.085 2.460 nonbonded pdb=" O LEU K 52 " pdb=" SG CYS K 53 " model vdw 2.390 3.400 nonbonded pdb=" O LYS I 27 " pdb=" OE1 GLU I 31 " model vdw 2.407 3.040 ... (remaining 196217 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 group one per residue 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: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.002 0.048 25848 Z= 0.121 Angle : 0.612 8.681 34865 Z= 0.323 Chirality : 0.040 0.169 3931 Planarity : 0.004 0.067 4463 Dihedral : 15.243 87.959 9760 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.06 % Favored : 93.50 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 3121 helix: 1.34 (0.12), residues: 1971 sheet: -0.81 (0.38), residues: 185 loop : -2.19 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 29 TYR 0.025 0.001 TYR J 432 PHE 0.037 0.001 PHE A 316 TRP 0.021 0.001 TRP B 427 HIS 0.004 0.001 HIS D 360 Details of bonding type rmsd covalent geometry : bond 0.00245 (25837) covalent geometry : angle 0.61133 (34859) hydrogen bonds : bond 0.12171 ( 1484) hydrogen bonds : angle 5.00976 ( 4347) metal coordination : bond 0.00660 ( 11) metal coordination : angle 2.94062 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 HIS cc_start: 0.8518 (m90) cc_final: 0.8232 (m90) REVERT: C 21 MET cc_start: 0.8596 (mmp) cc_final: 0.8338 (mmp) REVERT: C 68 MET cc_start: 0.8784 (ptp) cc_final: 0.8525 (mpp) REVERT: C 166 MET cc_start: 0.7076 (mpp) cc_final: 0.6473 (mpp) REVERT: D 1 MET cc_start: 0.6423 (ppp) cc_final: 0.6135 (mmt) REVERT: D 52 MET cc_start: 0.6840 (mpp) cc_final: 0.6462 (mpp) REVERT: D 267 MET cc_start: 0.8532 (tpp) cc_final: 0.8281 (mmt) REVERT: E 90 MET cc_start: 0.7562 (mpp) cc_final: 0.7220 (mpp) REVERT: E 117 MET cc_start: 0.8425 (ttt) cc_final: 0.8155 (ttp) REVERT: E 146 TRP cc_start: 0.8445 (p-90) cc_final: 0.8068 (p-90) REVERT: E 156 MET cc_start: 0.8546 (mmp) cc_final: 0.8266 (tmm) REVERT: E 165 PHE cc_start: 0.7295 (t80) cc_final: 0.6812 (t80) REVERT: F 87 PHE cc_start: 0.7933 (m-10) cc_final: 0.7662 (m-10) REVERT: F 106 TYR cc_start: 0.8609 (m-80) cc_final: 0.8355 (m-80) REVERT: F 273 ASP cc_start: 0.8220 (p0) cc_final: 0.7884 (p0) REVERT: H 50 MET cc_start: 0.8051 (mmp) cc_final: 0.7835 (mmm) REVERT: H 96 HIS cc_start: 0.6720 (t70) cc_final: 0.6506 (t70) REVERT: I 1 MET cc_start: 0.7952 (mmp) cc_final: 0.7619 (mmp) REVERT: I 50 MET cc_start: 0.6566 (mmm) cc_final: 0.6347 (mmm) REVERT: I 52 ASP cc_start: 0.7806 (m-30) cc_final: 0.7059 (p0) REVERT: J 313 MET cc_start: 0.1269 (tpt) cc_final: 0.0753 (ttt) REVERT: J 484 MET cc_start: 0.8717 (tpt) cc_final: 0.8120 (tpt) REVERT: J 715 LYS cc_start: 0.7908 (tppt) cc_final: 0.7706 (tppt) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.1864 time to fit residues: 54.8189 Evaluate side-chains 151 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN F 303 ASN J 435 HIS J 719 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.068672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.056943 restraints weight = 199627.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056880 restraints weight = 116880.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.057272 restraints weight = 82560.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057433 restraints weight = 68515.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057441 restraints weight = 61843.412| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25848 Z= 0.196 Angle : 0.631 11.898 34865 Z= 0.326 Chirality : 0.041 0.171 3931 Planarity : 0.004 0.052 4463 Dihedral : 4.314 35.641 3418 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.50 % Favored : 93.08 % Rotamer: Outliers : 0.47 % Allowed : 7.16 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 3121 helix: 1.35 (0.12), residues: 1999 sheet: -1.01 (0.40), residues: 168 loop : -2.11 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 29 TYR 0.019 0.002 TYR E 137 PHE 0.031 0.002 PHE F 112 TRP 0.039 0.002 TRP K 101 HIS 0.011 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00433 (25837) covalent geometry : angle 0.63074 (34859) hydrogen bonds : bond 0.04162 ( 1484) hydrogen bonds : angle 4.26048 ( 4347) metal coordination : bond 0.01655 ( 11) metal coordination : angle 2.30095 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 HIS cc_start: 0.8578 (m90) cc_final: 0.8223 (m90) REVERT: B 287 MET cc_start: 0.8584 (ptp) cc_final: 0.8216 (ttp) REVERT: C 21 MET cc_start: 0.8891 (mmp) cc_final: 0.8586 (mmp) REVERT: C 220 MET cc_start: 0.8505 (mtp) cc_final: 0.8237 (ttm) REVERT: D 1 MET cc_start: 0.6574 (ppp) cc_final: 0.6282 (mmp) REVERT: D 245 MET cc_start: 0.9021 (tpp) cc_final: 0.8527 (tpt) REVERT: D 267 MET cc_start: 0.8603 (tpp) cc_final: 0.8285 (mmt) REVERT: D 342 MET cc_start: 0.9223 (mmm) cc_final: 0.8976 (mmm) REVERT: E 67 MET cc_start: 0.8550 (ptp) cc_final: 0.8342 (ppp) REVERT: E 90 MET cc_start: 0.7794 (mpp) cc_final: 0.7358 (mpp) REVERT: E 117 MET cc_start: 0.8648 (ttt) cc_final: 0.8302 (ttp) REVERT: E 146 TRP cc_start: 0.8681 (p-90) cc_final: 0.8179 (p-90) REVERT: E 156 MET cc_start: 0.8778 (mmt) cc_final: 0.8367 (tmm) REVERT: E 165 PHE cc_start: 0.7504 (t80) cc_final: 0.6946 (t80) REVERT: E 234 ASP cc_start: 0.8858 (t0) cc_final: 0.8614 (t0) REVERT: F 106 TYR cc_start: 0.8760 (m-80) cc_final: 0.8479 (m-80) REVERT: F 206 MET cc_start: 0.8315 (mtt) cc_final: 0.8086 (ptp) REVERT: F 273 ASP cc_start: 0.8283 (p0) cc_final: 0.7921 (p0) REVERT: H 96 HIS cc_start: 0.6810 (t70) cc_final: 0.6512 (t70) REVERT: I 1 MET cc_start: 0.8426 (mmp) cc_final: 0.8035 (mmp) REVERT: I 4 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8861 (mmmt) REVERT: I 50 MET cc_start: 0.7008 (mmm) cc_final: 0.6768 (mmm) REVERT: J 313 MET cc_start: 0.1050 (tpt) cc_final: 0.0513 (ttt) REVERT: J 416 MET cc_start: 0.8111 (tmm) cc_final: 0.7888 (tmm) REVERT: K 89 LYS cc_start: 0.9134 (mmpt) cc_final: 0.8866 (mmmm) outliers start: 13 outliers final: 7 residues processed: 168 average time/residue: 0.1814 time to fit residues: 47.5500 Evaluate side-chains 159 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 739 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 230 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 297 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS H 47 HIS J 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.068384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.056748 restraints weight = 200005.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.056659 restraints weight = 116989.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.057170 restraints weight = 82921.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057232 restraints weight = 66811.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.057326 restraints weight = 59537.797| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25848 Z= 0.149 Angle : 0.581 12.750 34865 Z= 0.298 Chirality : 0.040 0.175 3931 Planarity : 0.004 0.053 4463 Dihedral : 4.257 33.634 3418 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.28 % Favored : 93.30 % Rotamer: Outliers : 0.90 % Allowed : 10.36 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 3121 helix: 1.47 (0.12), residues: 2000 sheet: -0.95 (0.39), residues: 177 loop : -2.12 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 204 TYR 0.016 0.001 TYR E 261 PHE 0.029 0.001 PHE F 112 TRP 0.024 0.001 TRP K 101 HIS 0.005 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00330 (25837) covalent geometry : angle 0.58094 (34859) hydrogen bonds : bond 0.03693 ( 1484) hydrogen bonds : angle 4.05631 ( 4347) metal coordination : bond 0.01129 ( 11) metal coordination : angle 1.85678 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8725 (tmm) cc_final: 0.8417 (tmm) REVERT: B 223 HIS cc_start: 0.8614 (m90) cc_final: 0.8265 (m90) REVERT: C 68 MET cc_start: 0.8948 (ptp) cc_final: 0.8665 (mpp) REVERT: C 214 MET cc_start: 0.7963 (pmm) cc_final: 0.7685 (ppp) REVERT: C 220 MET cc_start: 0.8369 (mtp) cc_final: 0.8127 (mtm) REVERT: D 1 MET cc_start: 0.6613 (ppp) cc_final: 0.6341 (mmp) REVERT: D 52 MET cc_start: 0.7021 (mpp) cc_final: 0.6584 (mpp) REVERT: D 245 MET cc_start: 0.9012 (tpp) cc_final: 0.8561 (tpt) REVERT: D 267 MET cc_start: 0.8589 (tpp) cc_final: 0.8273 (mmt) REVERT: D 342 MET cc_start: 0.9269 (mmm) cc_final: 0.9054 (mmm) REVERT: E 90 MET cc_start: 0.7787 (mpp) cc_final: 0.7280 (mpp) REVERT: E 93 MET cc_start: 0.6986 (pmm) cc_final: 0.5822 (pmm) REVERT: E 146 TRP cc_start: 0.8658 (p-90) cc_final: 0.8153 (p-90) REVERT: E 156 MET cc_start: 0.8780 (mmt) cc_final: 0.8442 (tmm) REVERT: E 157 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.7812 (pt) REVERT: E 165 PHE cc_start: 0.7428 (t80) cc_final: 0.6929 (t80) REVERT: E 234 ASP cc_start: 0.8931 (t0) cc_final: 0.8660 (t0) REVERT: F 106 TYR cc_start: 0.8735 (m-80) cc_final: 0.8500 (m-80) REVERT: F 273 ASP cc_start: 0.8222 (p0) cc_final: 0.7827 (p0) REVERT: F 302 MET cc_start: 0.9031 (tpp) cc_final: 0.8739 (tpp) REVERT: G 74 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8235 (t) REVERT: H 50 MET cc_start: 0.7533 (tpp) cc_final: 0.7175 (mmm) REVERT: H 96 HIS cc_start: 0.6807 (t70) cc_final: 0.6434 (t70) REVERT: H 146 LYS cc_start: 0.9277 (mtmm) cc_final: 0.9065 (mttt) REVERT: I 1 MET cc_start: 0.8396 (mmp) cc_final: 0.7969 (mmp) REVERT: I 52 ASP cc_start: 0.7907 (m-30) cc_final: 0.6997 (p0) REVERT: J 313 MET cc_start: 0.0735 (tpt) cc_final: 0.0244 (ttt) REVERT: K 89 LYS cc_start: 0.9215 (mmpt) cc_final: 0.8946 (mmmm) outliers start: 25 outliers final: 8 residues processed: 176 average time/residue: 0.1751 time to fit residues: 48.7406 Evaluate side-chains 160 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 341 TYR Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain K residue 88 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 25 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 220 HIS G 196 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 HIS J 664 GLN J 670 HIS K 48 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.054857 restraints weight = 198052.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.054723 restraints weight = 111371.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.055004 restraints weight = 84046.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.055146 restraints weight = 67564.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.055320 restraints weight = 61140.231| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25848 Z= 0.232 Angle : 0.665 13.085 34865 Z= 0.342 Chirality : 0.043 0.202 3931 Planarity : 0.004 0.072 4463 Dihedral : 4.498 28.250 3418 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.89 % Favored : 92.69 % Rotamer: Outliers : 1.58 % Allowed : 12.81 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3121 helix: 1.26 (0.12), residues: 2008 sheet: -1.04 (0.41), residues: 166 loop : -2.10 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 135 TYR 0.028 0.002 TYR E 137 PHE 0.028 0.002 PHE F 112 TRP 0.026 0.002 TRP K 101 HIS 0.007 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00516 (25837) covalent geometry : angle 0.66389 (34859) hydrogen bonds : bond 0.04267 ( 1484) hydrogen bonds : angle 4.31202 ( 4347) metal coordination : bond 0.02217 ( 11) metal coordination : angle 3.22160 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7304 (tpp-160) cc_final: 0.7066 (tpp-160) REVERT: B 89 MET cc_start: 0.8931 (mpp) cc_final: 0.8606 (mpp) REVERT: B 223 HIS cc_start: 0.8729 (m90) cc_final: 0.8380 (m90) REVERT: B 308 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8355 (pt) REVERT: C 21 MET cc_start: 0.8959 (mmp) cc_final: 0.8747 (mmp) REVERT: C 341 MET cc_start: 0.8147 (mmm) cc_final: 0.7921 (mmm) REVERT: D 1 MET cc_start: 0.6692 (ppp) cc_final: 0.6415 (mmp) REVERT: D 245 MET cc_start: 0.9091 (tpp) cc_final: 0.8688 (tpt) REVERT: D 267 MET cc_start: 0.8704 (tpp) cc_final: 0.8399 (mmt) REVERT: E 90 MET cc_start: 0.7938 (mpp) cc_final: 0.7368 (mpp) REVERT: E 146 TRP cc_start: 0.8857 (p-90) cc_final: 0.8361 (p-90) REVERT: E 156 MET cc_start: 0.8839 (mmt) cc_final: 0.8450 (tmm) REVERT: E 157 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.7852 (pt) REVERT: E 234 ASP cc_start: 0.9080 (t0) cc_final: 0.8802 (t0) REVERT: F 106 TYR cc_start: 0.8729 (m-10) cc_final: 0.8518 (m-80) REVERT: F 273 ASP cc_start: 0.8303 (p0) cc_final: 0.8024 (p0) REVERT: F 302 MET cc_start: 0.9133 (tpp) cc_final: 0.8855 (tpp) REVERT: H 50 MET cc_start: 0.7533 (tpp) cc_final: 0.7216 (mmm) REVERT: H 96 HIS cc_start: 0.6903 (t70) cc_final: 0.6455 (t70) REVERT: H 146 LYS cc_start: 0.9265 (mtmm) cc_final: 0.8888 (mttt) REVERT: H 200 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8139 (mm) REVERT: I 1 MET cc_start: 0.8688 (mmp) cc_final: 0.7504 (mmp) REVERT: J 313 MET cc_start: 0.0704 (tpt) cc_final: 0.0224 (ttt) REVERT: K 89 LYS cc_start: 0.9291 (mmpt) cc_final: 0.8978 (mmmm) outliers start: 44 outliers final: 17 residues processed: 192 average time/residue: 0.1703 time to fit residues: 52.1970 Evaluate side-chains 169 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain K residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN E 158 ASN E 243 ASN J 435 HIS J 598 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.067489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.055815 restraints weight = 198191.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.055794 restraints weight = 124371.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.056038 restraints weight = 89670.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.056204 restraints weight = 71914.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.056284 restraints weight = 62599.578| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25848 Z= 0.131 Angle : 0.593 13.831 34865 Z= 0.300 Chirality : 0.040 0.319 3931 Planarity : 0.004 0.050 4463 Dihedral : 4.318 27.681 3418 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 1.55 % Allowed : 14.21 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 3121 helix: 1.47 (0.12), residues: 2003 sheet: -0.88 (0.41), residues: 166 loop : -2.10 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 29 TYR 0.013 0.001 TYR J 753 PHE 0.024 0.001 PHE F 112 TRP 0.018 0.001 TRP K 101 HIS 0.006 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00290 (25837) covalent geometry : angle 0.59268 (34859) hydrogen bonds : bond 0.03581 ( 1484) hydrogen bonds : angle 4.05103 ( 4347) metal coordination : bond 0.00663 ( 11) metal coordination : angle 2.00218 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7307 (tpp-160) cc_final: 0.6966 (tpp-160) REVERT: B 223 HIS cc_start: 0.8724 (m90) cc_final: 0.8390 (m90) REVERT: B 308 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8314 (pt) REVERT: C 68 MET cc_start: 0.9005 (ptp) cc_final: 0.8706 (mpp) REVERT: C 228 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8575 (tp) REVERT: D 1 MET cc_start: 0.6723 (ppp) cc_final: 0.6493 (mmp) REVERT: D 245 MET cc_start: 0.9003 (tpp) cc_final: 0.8611 (tpt) REVERT: D 267 MET cc_start: 0.8659 (tpp) cc_final: 0.8309 (mmt) REVERT: E 90 MET cc_start: 0.7839 (mpp) cc_final: 0.7257 (mpp) REVERT: E 146 TRP cc_start: 0.8767 (p-90) cc_final: 0.8389 (p-90) REVERT: E 156 MET cc_start: 0.8789 (mmt) cc_final: 0.8417 (tmm) REVERT: E 157 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.7781 (pt) REVERT: E 174 ARG cc_start: 0.9285 (mtt-85) cc_final: 0.8810 (ttm-80) REVERT: E 243 ASN cc_start: 0.7047 (OUTLIER) cc_final: 0.6724 (p0) REVERT: F 106 TYR cc_start: 0.8652 (m-10) cc_final: 0.8420 (m-80) REVERT: F 267 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8436 (mm) REVERT: F 273 ASP cc_start: 0.8189 (p0) cc_final: 0.7834 (p0) REVERT: H 50 MET cc_start: 0.7471 (tpp) cc_final: 0.7119 (mmm) REVERT: H 96 HIS cc_start: 0.6906 (t70) cc_final: 0.6450 (t70) REVERT: I 1 MET cc_start: 0.8285 (mmp) cc_final: 0.7786 (mmp) REVERT: J 313 MET cc_start: 0.0624 (tpt) cc_final: 0.0167 (ttt) REVERT: K 89 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8912 (mmmm) outliers start: 43 outliers final: 22 residues processed: 189 average time/residue: 0.1692 time to fit residues: 50.7541 Evaluate side-chains 177 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain J residue 767 VAL Chi-restraints excluded: chain K residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 221 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 257 optimal weight: 0.0170 chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN F 50 ASN G 93 GLN J 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.068096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.056434 restraints weight = 199219.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.056377 restraints weight = 118650.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.056728 restraints weight = 87562.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056764 restraints weight = 79343.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.056868 restraints weight = 65894.805| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25848 Z= 0.110 Angle : 0.590 14.523 34865 Z= 0.295 Chirality : 0.040 0.334 3931 Planarity : 0.004 0.049 4463 Dihedral : 4.196 28.289 3418 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.34 % Favored : 93.30 % Rotamer: Outliers : 1.44 % Allowed : 15.36 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 3121 helix: 1.57 (0.12), residues: 2003 sheet: -0.73 (0.41), residues: 171 loop : -2.03 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 29 TYR 0.013 0.001 TYR J 753 PHE 0.022 0.001 PHE D 48 TRP 0.015 0.001 TRP K 101 HIS 0.014 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00237 (25837) covalent geometry : angle 0.58924 (34859) hydrogen bonds : bond 0.03331 ( 1484) hydrogen bonds : angle 3.95691 ( 4347) metal coordination : bond 0.00305 ( 11) metal coordination : angle 1.71852 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.7758 (mmt) cc_final: 0.7441 (mmm) REVERT: B 223 HIS cc_start: 0.8715 (m90) cc_final: 0.8393 (m90) REVERT: B 308 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8292 (pt) REVERT: C 21 MET cc_start: 0.9044 (mmp) cc_final: 0.8833 (mmp) REVERT: C 68 MET cc_start: 0.9008 (ptp) cc_final: 0.8696 (mpp) REVERT: D 1 MET cc_start: 0.6784 (ppp) cc_final: 0.6517 (mmp) REVERT: D 52 MET cc_start: 0.7325 (mpp) cc_final: 0.6877 (mpp) REVERT: D 245 MET cc_start: 0.8978 (tpp) cc_final: 0.8573 (tpt) REVERT: D 267 MET cc_start: 0.8652 (tpp) cc_final: 0.8306 (mmt) REVERT: E 90 MET cc_start: 0.7855 (mpp) cc_final: 0.7261 (mpp) REVERT: E 146 TRP cc_start: 0.8765 (p-90) cc_final: 0.8338 (p-90) REVERT: E 156 MET cc_start: 0.8810 (mmt) cc_final: 0.8598 (mmt) REVERT: E 174 ARG cc_start: 0.9291 (mtt-85) cc_final: 0.8809 (ttm-80) REVERT: F 106 TYR cc_start: 0.8679 (m-10) cc_final: 0.8440 (m-80) REVERT: F 157 MET cc_start: 0.7995 (mmp) cc_final: 0.7767 (mmp) REVERT: F 267 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8371 (mm) REVERT: F 273 ASP cc_start: 0.8198 (p0) cc_final: 0.7786 (p0) REVERT: G 74 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8145 (p) REVERT: H 50 MET cc_start: 0.7459 (tpp) cc_final: 0.7085 (mmm) REVERT: H 96 HIS cc_start: 0.7029 (t70) cc_final: 0.6481 (t70) REVERT: H 208 GLU cc_start: 0.6155 (pt0) cc_final: 0.5154 (tt0) REVERT: I 1 MET cc_start: 0.8194 (mmp) cc_final: 0.7643 (mmp) REVERT: J 313 MET cc_start: 0.0694 (tpt) cc_final: 0.0216 (ttt) REVERT: K 89 LYS cc_start: 0.9127 (mmpt) cc_final: 0.8892 (mmmm) outliers start: 40 outliers final: 23 residues processed: 193 average time/residue: 0.1703 time to fit residues: 51.9664 Evaluate side-chains 180 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 719 HIS Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain J residue 767 VAL Chi-restraints excluded: chain K residue 88 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 268 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.067777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056120 restraints weight = 197764.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.056192 restraints weight = 110867.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.056503 restraints weight = 78988.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.056711 restraints weight = 66230.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.056741 restraints weight = 58555.946| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25848 Z= 0.125 Angle : 0.603 14.303 34865 Z= 0.302 Chirality : 0.040 0.347 3931 Planarity : 0.004 0.046 4463 Dihedral : 4.178 27.418 3418 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.31 % Favored : 93.34 % Rotamer: Outliers : 1.55 % Allowed : 15.72 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 3121 helix: 1.58 (0.12), residues: 2009 sheet: -0.69 (0.41), residues: 171 loop : -2.01 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 29 TYR 0.012 0.001 TYR J 753 PHE 0.024 0.001 PHE D 48 TRP 0.021 0.001 TRP K 101 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00280 (25837) covalent geometry : angle 0.60240 (34859) hydrogen bonds : bond 0.03337 ( 1484) hydrogen bonds : angle 3.95194 ( 4347) metal coordination : bond 0.00625 ( 11) metal coordination : angle 1.94820 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 HIS cc_start: 0.8737 (m90) cc_final: 0.8425 (m90) REVERT: B 308 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8338 (pt) REVERT: C 21 MET cc_start: 0.9151 (mmp) cc_final: 0.8882 (mmp) REVERT: C 68 MET cc_start: 0.8994 (ptp) cc_final: 0.8739 (mpp) REVERT: C 341 MET cc_start: 0.8103 (mmm) cc_final: 0.7853 (mmm) REVERT: D 1 MET cc_start: 0.6733 (ppp) cc_final: 0.6497 (mmp) REVERT: D 245 MET cc_start: 0.9013 (tpp) cc_final: 0.8599 (tpt) REVERT: D 267 MET cc_start: 0.8667 (tpp) cc_final: 0.8301 (mmt) REVERT: E 90 MET cc_start: 0.7881 (mpp) cc_final: 0.7278 (mpp) REVERT: E 146 TRP cc_start: 0.8755 (p-90) cc_final: 0.8325 (p-90) REVERT: E 156 MET cc_start: 0.8789 (mmt) cc_final: 0.8568 (mmt) REVERT: E 174 ARG cc_start: 0.9269 (mtt-85) cc_final: 0.8774 (ttm-80) REVERT: F 106 TYR cc_start: 0.8642 (m-10) cc_final: 0.8416 (m-80) REVERT: F 157 MET cc_start: 0.7931 (mmp) cc_final: 0.7707 (mmp) REVERT: G 74 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8191 (p) REVERT: H 50 MET cc_start: 0.7492 (tpp) cc_final: 0.7132 (mmm) REVERT: H 96 HIS cc_start: 0.7040 (t70) cc_final: 0.6499 (t70) REVERT: I 1 MET cc_start: 0.8156 (mmp) cc_final: 0.7579 (mmp) REVERT: J 313 MET cc_start: 0.0902 (tpt) cc_final: 0.0402 (ttt) REVERT: J 504 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7638 (p) outliers start: 43 outliers final: 27 residues processed: 188 average time/residue: 0.1584 time to fit residues: 47.7519 Evaluate side-chains 178 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 719 HIS Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 101 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 165 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 chunk 289 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN C 20 GLN E 243 ASN J 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.067984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.055846 restraints weight = 197035.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.056142 restraints weight = 117532.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.056232 restraints weight = 86768.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.056311 restraints weight = 78733.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057108 restraints weight = 66406.381| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25848 Z= 0.121 Angle : 0.612 14.718 34865 Z= 0.306 Chirality : 0.040 0.360 3931 Planarity : 0.004 0.047 4463 Dihedral : 4.150 27.503 3418 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.31 % Favored : 93.34 % Rotamer: Outliers : 1.55 % Allowed : 15.68 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3121 helix: 1.60 (0.12), residues: 2011 sheet: -0.60 (0.41), residues: 171 loop : -1.98 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 29 TYR 0.013 0.001 TYR J 753 PHE 0.019 0.001 PHE A 81 TRP 0.020 0.001 TRP K 101 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00268 (25837) covalent geometry : angle 0.61137 (34859) hydrogen bonds : bond 0.03299 ( 1484) hydrogen bonds : angle 3.94728 ( 4347) metal coordination : bond 0.00593 ( 11) metal coordination : angle 1.91152 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.9370 (ppp) cc_final: 0.8735 (pmm) REVERT: B 223 HIS cc_start: 0.8738 (m90) cc_final: 0.8422 (m90) REVERT: B 308 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (pt) REVERT: C 68 MET cc_start: 0.8997 (ptp) cc_final: 0.8728 (mpp) REVERT: C 167 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7308 (mmm) REVERT: D 1 MET cc_start: 0.6834 (ppp) cc_final: 0.6612 (mmp) REVERT: D 245 MET cc_start: 0.9014 (tpp) cc_final: 0.8600 (tpt) REVERT: D 267 MET cc_start: 0.8665 (tpp) cc_final: 0.8288 (mmt) REVERT: D 385 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4297 (mt) REVERT: E 90 MET cc_start: 0.7937 (mpp) cc_final: 0.7308 (mpp) REVERT: E 146 TRP cc_start: 0.8826 (p-90) cc_final: 0.8381 (p-90) REVERT: E 156 MET cc_start: 0.8844 (mmt) cc_final: 0.8456 (tmm) REVERT: E 174 ARG cc_start: 0.9287 (mtt-85) cc_final: 0.8821 (ttm-80) REVERT: E 234 ASP cc_start: 0.9116 (t0) cc_final: 0.8858 (t0) REVERT: E 298 ASP cc_start: 0.4052 (OUTLIER) cc_final: 0.1572 (t0) REVERT: F 106 TYR cc_start: 0.8704 (m-10) cc_final: 0.8456 (m-80) REVERT: F 157 MET cc_start: 0.8072 (mmp) cc_final: 0.7870 (mmp) REVERT: F 267 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8377 (mm) REVERT: G 74 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8201 (p) REVERT: H 50 MET cc_start: 0.7469 (tpp) cc_final: 0.7141 (mmm) REVERT: H 96 HIS cc_start: 0.7138 (t70) cc_final: 0.6551 (t70) REVERT: H 151 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8972 (mp10) REVERT: I 1 MET cc_start: 0.8278 (mmp) cc_final: 0.7670 (mmp) REVERT: J 313 MET cc_start: 0.0804 (tpt) cc_final: 0.0337 (ttt) REVERT: J 504 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7564 (p) outliers start: 43 outliers final: 28 residues processed: 186 average time/residue: 0.1629 time to fit residues: 48.8126 Evaluate side-chains 183 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 101 TRP Chi-restraints excluded: chain K residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 274 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 465 HIS ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS C 20 GLN ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS J 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.066757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.054832 restraints weight = 195740.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.055060 restraints weight = 104855.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.055184 restraints weight = 84355.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.055317 restraints weight = 69468.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.055719 restraints weight = 59542.961| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25848 Z= 0.195 Angle : 0.676 14.646 34865 Z= 0.340 Chirality : 0.042 0.364 3931 Planarity : 0.004 0.069 4463 Dihedral : 4.328 25.162 3418 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.86 % Favored : 92.82 % Rotamer: Outliers : 1.69 % Allowed : 15.86 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 3121 helix: 1.49 (0.12), residues: 2017 sheet: -0.69 (0.41), residues: 169 loop : -2.00 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 165 TYR 0.017 0.001 TYR D 114 PHE 0.018 0.002 PHE A 81 TRP 0.029 0.002 TRP K 101 HIS 0.007 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00435 (25837) covalent geometry : angle 0.67501 (34859) hydrogen bonds : bond 0.03813 ( 1484) hydrogen bonds : angle 4.14082 ( 4347) metal coordination : bond 0.01346 ( 11) metal coordination : angle 2.79689 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 HIS cc_start: 0.8697 (m90) cc_final: 0.8410 (m90) REVERT: B 285 MET cc_start: 0.8069 (mmp) cc_final: 0.7835 (mmm) REVERT: B 308 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8415 (pt) REVERT: C 21 MET cc_start: 0.9242 (mmp) cc_final: 0.8890 (mmp) REVERT: C 68 MET cc_start: 0.8999 (ptp) cc_final: 0.8763 (mpp) REVERT: D 52 MET cc_start: 0.7437 (mpp) cc_final: 0.7014 (mpp) REVERT: D 245 MET cc_start: 0.9033 (tpp) cc_final: 0.8648 (tpt) REVERT: D 267 MET cc_start: 0.8708 (tpp) cc_final: 0.8362 (mmt) REVERT: E 90 MET cc_start: 0.7733 (mpp) cc_final: 0.7157 (mpp) REVERT: E 146 TRP cc_start: 0.8804 (p-90) cc_final: 0.8408 (p-90) REVERT: E 156 MET cc_start: 0.8762 (mmt) cc_final: 0.8393 (tmm) REVERT: E 174 ARG cc_start: 0.9206 (mtt-85) cc_final: 0.8731 (ttm-80) REVERT: E 234 ASP cc_start: 0.9070 (t0) cc_final: 0.8843 (t0) REVERT: E 298 ASP cc_start: 0.4088 (OUTLIER) cc_final: 0.0590 (t0) REVERT: F 106 TYR cc_start: 0.8580 (m-10) cc_final: 0.8369 (m-80) REVERT: F 157 MET cc_start: 0.8042 (mmp) cc_final: 0.7832 (mmp) REVERT: F 273 ASP cc_start: 0.8219 (p0) cc_final: 0.7887 (p0) REVERT: G 74 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8439 (p) REVERT: H 151 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8839 (mp10) REVERT: I 1 MET cc_start: 0.8238 (mmp) cc_final: 0.7577 (mmp) REVERT: J 313 MET cc_start: 0.0884 (tpt) cc_final: 0.0366 (ttt) REVERT: J 504 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7694 (p) outliers start: 47 outliers final: 33 residues processed: 184 average time/residue: 0.1607 time to fit residues: 48.1327 Evaluate side-chains 184 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 721 VAL Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 101 TRP Chi-restraints excluded: chain K residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 17 optimal weight: 0.0050 chunk 239 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 35 optimal weight: 0.3980 chunk 308 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.066703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.054557 restraints weight = 195052.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.054791 restraints weight = 108290.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.055017 restraints weight = 81921.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.055047 restraints weight = 74961.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.055294 restraints weight = 62674.637| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25848 Z= 0.186 Angle : 0.671 15.005 34865 Z= 0.336 Chirality : 0.042 0.379 3931 Planarity : 0.004 0.052 4463 Dihedral : 4.363 26.466 3418 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.86 % Favored : 92.82 % Rotamer: Outliers : 1.51 % Allowed : 16.01 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 3121 helix: 1.44 (0.12), residues: 2017 sheet: -0.67 (0.41), residues: 169 loop : -2.04 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 29 TYR 0.014 0.001 TYR E 261 PHE 0.046 0.002 PHE A 81 TRP 0.025 0.002 TRP K 101 HIS 0.023 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00417 (25837) covalent geometry : angle 0.67050 (34859) hydrogen bonds : bond 0.03772 ( 1484) hydrogen bonds : angle 4.19402 ( 4347) metal coordination : bond 0.01214 ( 11) metal coordination : angle 2.78974 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 HIS cc_start: 0.8757 (m90) cc_final: 0.8413 (m90) REVERT: B 285 MET cc_start: 0.8028 (mmp) cc_final: 0.7808 (mmm) REVERT: B 308 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8407 (pt) REVERT: C 20 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: C 21 MET cc_start: 0.9244 (mmp) cc_final: 0.8814 (mmp) REVERT: D 245 MET cc_start: 0.9027 (tpp) cc_final: 0.8648 (tpt) REVERT: D 267 MET cc_start: 0.8717 (tpp) cc_final: 0.8396 (mmt) REVERT: E 67 MET cc_start: 0.8930 (pmm) cc_final: 0.8652 (pmm) REVERT: E 90 MET cc_start: 0.7885 (mpp) cc_final: 0.7291 (mpp) REVERT: E 146 TRP cc_start: 0.8901 (p-90) cc_final: 0.8547 (p-90) REVERT: E 156 MET cc_start: 0.8854 (mmt) cc_final: 0.8446 (tmm) REVERT: E 174 ARG cc_start: 0.9227 (mtt-85) cc_final: 0.8754 (ttm-80) REVERT: E 234 ASP cc_start: 0.9153 (t0) cc_final: 0.8904 (t0) REVERT: E 298 ASP cc_start: 0.4215 (OUTLIER) cc_final: 0.0551 (t0) REVERT: F 106 TYR cc_start: 0.8694 (m-10) cc_final: 0.8471 (m-80) REVERT: F 157 MET cc_start: 0.8197 (mmp) cc_final: 0.7911 (mmp) REVERT: F 273 ASP cc_start: 0.8207 (p0) cc_final: 0.7871 (p0) REVERT: G 74 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8442 (p) REVERT: H 151 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8834 (mp10) REVERT: I 1 MET cc_start: 0.8262 (mmp) cc_final: 0.7549 (mmp) REVERT: J 313 MET cc_start: 0.0806 (tpt) cc_final: 0.0291 (ttt) REVERT: J 504 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7661 (p) REVERT: J 697 ASP cc_start: 0.8220 (t0) cc_final: 0.7831 (p0) outliers start: 42 outliers final: 33 residues processed: 180 average time/residue: 0.1688 time to fit residues: 48.8260 Evaluate side-chains 181 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 701 HIS Chi-restraints excluded: chain J residue 721 VAL Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 101 TRP Chi-restraints excluded: chain K residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.066652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.054606 restraints weight = 194716.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.054932 restraints weight = 104454.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.055233 restraints weight = 76549.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055317 restraints weight = 64369.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.055513 restraints weight = 56872.895| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25848 Z= 0.171 Angle : 0.664 14.831 34865 Z= 0.333 Chirality : 0.042 0.380 3931 Planarity : 0.004 0.050 4463 Dihedral : 4.364 27.200 3418 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.79 % Favored : 92.89 % Rotamer: Outliers : 1.37 % Allowed : 16.44 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 3121 helix: 1.47 (0.12), residues: 2015 sheet: -0.75 (0.40), residues: 174 loop : -2.04 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 29 TYR 0.014 0.001 TYR J 753 PHE 0.047 0.001 PHE A 81 TRP 0.024 0.001 TRP K 101 HIS 0.008 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00384 (25837) covalent geometry : angle 0.66345 (34859) hydrogen bonds : bond 0.03731 ( 1484) hydrogen bonds : angle 4.18031 ( 4347) metal coordination : bond 0.01044 ( 11) metal coordination : angle 2.72434 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.52 seconds wall clock time: 68 minutes 12.08 seconds (4092.08 seconds total)