Starting phenix.real_space_refine on Mon Jan 20 07:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izw_61044/01_2025/9izw_61044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izw_61044/01_2025/9izw_61044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izw_61044/01_2025/9izw_61044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izw_61044/01_2025/9izw_61044.map" model { file = "/net/cci-nas-00/data/ceres_data/9izw_61044/01_2025/9izw_61044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izw_61044/01_2025/9izw_61044.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 9644 2.51 5 N 2608 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15196 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3799 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "B" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3799 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3799 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "D" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3799 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Time building chain proxies: 9.04, per 1000 atoms: 0.59 Number of scatterers: 15196 At special positions: 0 Unit cell: (110.416, 112.888, 117.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2840 8.00 N 2608 7.00 C 9644 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: 4.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 19 sheets defined 41.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 43 through 63 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.575A pdb=" N LEU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.895A pdb=" N MET A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.686A pdb=" N HIS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.781A pdb=" N LYS A 298 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 299 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 328 through 346 removed outlier: 3.538A pdb=" N GLY A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.734A pdb=" N LEU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 432' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.947A pdb=" N ILE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 64 removed outlier: 3.587A pdb=" N ASP B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE B 51 " --> pdb=" O MET B 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.581A pdb=" N GLN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 4.010A pdb=" N ILE B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.617A pdb=" N GLU B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.805A pdb=" N MET B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 3.666A pdb=" N VAL B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.696A pdb=" N LEU B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.537A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.945A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 removed outlier: 4.112A pdb=" N THR B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 302 through 311 removed outlier: 3.917A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.605A pdb=" N LYS B 383 " --> pdb=" O MET B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 removed outlier: 4.061A pdb=" N GLN B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.778A pdb=" N ALA B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.999A pdb=" N GLN B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 471 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 65 through 83 removed outlier: 3.894A pdb=" N GLN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.698A pdb=" N LYS C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 118 removed outlier: 3.643A pdb=" N GLU C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.807A pdb=" N PHE C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Proline residue: C 165 - end of helix removed outlier: 3.759A pdb=" N VAL C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 removed outlier: 3.526A pdb=" N ALA C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 191 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.629A pdb=" N PHE C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.732A pdb=" N TYR C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.872A pdb=" N ALA C 281 " --> pdb=" O PHE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 299 removed outlier: 4.109A pdb=" N LYS C 298 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 299 " --> pdb=" O GLU C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 299' Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.808A pdb=" N LYS C 332 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 407 removed outlier: 3.598A pdb=" N ALA C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 431 removed outlier: 3.919A pdb=" N ALA C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 474 removed outlier: 3.560A pdb=" N ILE C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.515A pdb=" N ARG D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 Processing helix chain 'D' and resid 65 through 82 removed outlier: 3.806A pdb=" N VAL D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.757A pdb=" N ILE D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.533A pdb=" N VAL D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.864A pdb=" N MET D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 210 through 217 removed outlier: 3.590A pdb=" N ASN D 214 " --> pdb=" O HIS D 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS D 217 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 245 removed outlier: 4.078A pdb=" N TYR D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 removed outlier: 3.837A pdb=" N PHE D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.601A pdb=" N ASN D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 removed outlier: 3.619A pdb=" N LYS D 332 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 421 through 431 removed outlier: 3.505A pdb=" N LYS D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.824A pdb=" N ASP D 488 " --> pdb=" O LYS D 485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.992A pdb=" N GLY A 37 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 142 removed outlier: 3.685A pdb=" N ASP A 136 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.311A pdb=" N PHE A 174 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 146 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 225 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N GLN A 249 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 225 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 254 through 255 removed outlier: 6.698A pdb=" N ALA A 254 " --> pdb=" O ALA A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.956A pdb=" N THR A 370 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL A 393 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 372 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 439 removed outlier: 4.009A pdb=" N LEU B 137 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 126 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 29 removed outlier: 3.871A pdb=" N ILE B 25 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 37 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN B 29 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 35 " --> pdb=" O ASN B 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 203 through 205 removed outlier: 7.004A pdb=" N VAL B 146 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA B 224 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 228 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 247 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 290 through 293 removed outlier: 6.652A pdb=" N ALA B 291 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 372 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU B 395 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASN B 374 " --> pdb=" O GLU B 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.553A pdb=" N ILE C 12 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 15 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 28 removed outlier: 5.970A pdb=" N ILE C 25 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG C 38 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 27 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 142 removed outlier: 3.752A pdb=" N TYR C 138 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL D 437 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR C 479 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL D 439 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR C 481 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS D 257 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY D 258 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 294 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL D 260 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 396 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.501A pdb=" N PHE C 174 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS C 147 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS C 177 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY C 149 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 146 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA C 224 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS C 223 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLN C 249 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE C 225 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASN C 251 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE C 227 " --> pdb=" O ASN C 251 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 250 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 254 through 255 removed outlier: 7.226A pdb=" N ALA C 254 " --> pdb=" O ALA C 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 348 through 351 removed outlier: 6.524A pdb=" N ILE C 371 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 258 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS C 257 " --> pdb=" O GLY C 414 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR D 132 " --> pdb=" O MET D 135 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU D 137 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N SER D 130 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N SER D 139 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N MET D 128 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 24 through 28 removed outlier: 6.096A pdb=" N ILE D 25 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG D 38 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 27 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.838A pdb=" N PHE D 174 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 224 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 228 " --> pdb=" O ILE D 150 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1599 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: 5.17 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2573 1.31 - 1.44: 3779 1.44 - 1.56: 8980 1.56 - 1.68: 0 1.68 - 1.81: 176 Bond restraints: 15508 Sorted by residual: bond pdb=" CA VAL D 228 " pdb=" C VAL D 228 " ideal model delta sigma weight residual 1.522 1.438 0.084 1.24e-02 6.50e+03 4.55e+01 bond pdb=" N VAL D 228 " pdb=" CA VAL D 228 " ideal model delta sigma weight residual 1.458 1.394 0.064 1.19e-02 7.06e+03 2.87e+01 bond pdb=" CA VAL D 228 " pdb=" CB VAL D 228 " ideal model delta sigma weight residual 1.541 1.478 0.063 1.28e-02 6.10e+03 2.43e+01 bond pdb=" C VAL D 228 " pdb=" O VAL D 228 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.04e-02 9.25e+03 2.18e+01 bond pdb=" C GLY D 229 " pdb=" O GLY D 229 " ideal model delta sigma weight residual 1.232 1.191 0.041 1.13e-02 7.83e+03 1.33e+01 ... (remaining 15503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 20987 3.59 - 7.19: 35 7.19 - 10.78: 4 10.78 - 14.38: 1 14.38 - 17.97: 1 Bond angle restraints: 21028 Sorted by residual: angle pdb=" N VAL D 228 " pdb=" CA VAL D 228 " pdb=" C VAL D 228 " ideal model delta sigma weight residual 108.12 90.15 17.97 1.44e+00 4.82e-01 1.56e+02 angle pdb=" N GLY D 229 " pdb=" CA GLY D 229 " pdb=" C GLY D 229 " ideal model delta sigma weight residual 111.08 101.39 9.69 1.62e+00 3.81e-01 3.58e+01 angle pdb=" N ILE C 131 " pdb=" CA ILE C 131 " pdb=" C ILE C 131 " ideal model delta sigma weight residual 111.81 107.30 4.51 8.60e-01 1.35e+00 2.75e+01 angle pdb=" C TYR B 230 " pdb=" CA TYR B 230 " pdb=" CB TYR B 230 " ideal model delta sigma weight residual 113.15 102.28 10.87 2.38e+00 1.77e-01 2.09e+01 angle pdb=" C TYR D 230 " pdb=" CA TYR D 230 " pdb=" CB TYR D 230 " ideal model delta sigma weight residual 109.71 117.84 -8.13 1.80e+00 3.09e-01 2.04e+01 ... (remaining 21023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 8400 17.46 - 34.93: 749 34.93 - 52.39: 179 52.39 - 69.85: 41 69.85 - 87.31: 19 Dihedral angle restraints: 9388 sinusoidal: 3704 harmonic: 5684 Sorted by residual: dihedral pdb=" C TYR B 230 " pdb=" N TYR B 230 " pdb=" CA TYR B 230 " pdb=" CB TYR B 230 " ideal model delta harmonic sigma weight residual -122.60 -111.21 -11.39 0 2.50e+00 1.60e-01 2.08e+01 dihedral pdb=" N TYR B 230 " pdb=" C TYR B 230 " pdb=" CA TYR B 230 " pdb=" CB TYR B 230 " ideal model delta harmonic sigma weight residual 122.80 114.15 8.65 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" N VAL D 228 " pdb=" C VAL D 228 " pdb=" CA VAL D 228 " pdb=" CB VAL D 228 " ideal model delta harmonic sigma weight residual 123.40 115.11 8.29 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 9385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2146 0.072 - 0.145: 239 0.145 - 0.217: 1 0.217 - 0.290: 1 0.290 - 0.362: 1 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA ASN D 231 " pdb=" N ASN D 231 " pdb=" C ASN D 231 " pdb=" CB ASN D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA TYR B 230 " pdb=" N TYR B 230 " pdb=" C TYR B 230 " pdb=" CB TYR B 230 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA TYR D 230 " pdb=" N TYR D 230 " pdb=" C TYR D 230 " pdb=" CB TYR D 230 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2385 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 227 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C PHE D 227 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE D 227 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL D 228 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 230 " 0.035 2.00e-02 2.50e+03 2.00e-02 8.03e+00 pdb=" CG TYR D 230 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 230 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D 230 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 230 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 230 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 230 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 228 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL D 228 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL D 228 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY D 229 " 0.013 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 81 2.50 - 3.10: 10784 3.10 - 3.70: 23221 3.70 - 4.30: 34583 4.30 - 4.90: 57101 Nonbonded interactions: 125770 Sorted by model distance: nonbonded pdb=" OD2 ASP D 136 " pdb=" OH TYR D 138 " model vdw 1.895 3.040 nonbonded pdb=" OD1 ASP B 136 " pdb=" OG SER B 482 " model vdw 2.002 3.040 nonbonded pdb=" O ILE D 471 " pdb=" OG1 THR D 475 " model vdw 2.040 3.040 nonbonded pdb=" O ASP A 263 " pdb=" OG1 THR A 420 " model vdw 2.043 3.040 nonbonded pdb=" O ASP C 263 " pdb=" OG1 THR C 420 " model vdw 2.102 3.040 ... (remaining 125765 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.080 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 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 : 0.003 0.084 15508 Z= 0.167 Angle : 0.535 17.969 21028 Z= 0.311 Chirality : 0.042 0.362 2388 Planarity : 0.003 0.044 2736 Dihedral : 14.726 87.314 5740 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.34 % Allowed : 10.83 % Favored : 87.83 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.16), residues: 1988 helix: -1.58 (0.17), residues: 724 sheet: -2.45 (0.24), residues: 315 loop : -3.46 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 162 HIS 0.002 0.000 HIS B 115 PHE 0.012 0.001 PHE A 164 TYR 0.040 0.001 TYR D 230 ARG 0.002 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 396 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.7432 (m100) cc_final: 0.7162 (m100) REVERT: A 215 PHE cc_start: 0.7450 (t80) cc_final: 0.7078 (t80) REVERT: A 244 HIS cc_start: 0.5983 (m90) cc_final: 0.5703 (m-70) REVERT: A 413 ASN cc_start: 0.6278 (p0) cc_final: 0.5964 (t0) REVERT: B 93 LEU cc_start: 0.7468 (pp) cc_final: 0.7057 (mt) REVERT: B 105 ASP cc_start: 0.5425 (m-30) cc_final: 0.4832 (m-30) REVERT: B 286 MET cc_start: 0.1991 (pmm) cc_final: 0.1120 (pmm) REVERT: B 359 LYS cc_start: 0.5080 (OUTLIER) cc_final: 0.4006 (tttt) REVERT: C 55 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8004 (mtmt) REVERT: C 75 ARG cc_start: 0.7916 (tpt90) cc_final: 0.7706 (tpt-90) REVERT: C 78 GLN cc_start: 0.7392 (tt0) cc_final: 0.7133 (tm-30) REVERT: C 172 ASN cc_start: 0.6195 (m-40) cc_final: 0.5969 (m-40) REVERT: C 485 LYS cc_start: 0.2194 (OUTLIER) cc_final: 0.1824 (tppt) REVERT: D 154 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7035 (m-40) REVERT: D 337 ASN cc_start: 0.8473 (m-40) cc_final: 0.7052 (m-40) REVERT: D 487 GLU cc_start: 0.2748 (OUTLIER) cc_final: -0.0853 (mp0) outliers start: 22 outliers final: 8 residues processed: 413 average time/residue: 0.2929 time to fit residues: 173.9708 Evaluate side-chains 298 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 286 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 487 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 50 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 204 ASN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 HIS ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 194 GLN B 374 ASN B 421 ASN B 464 ASN C 70 GLN C 204 ASN C 249 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 436 GLN D 472 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.232236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.180199 restraints weight = 18794.358| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.11 r_work: 0.3814 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15508 Z= 0.446 Angle : 0.725 9.562 21028 Z= 0.372 Chirality : 0.051 0.277 2388 Planarity : 0.005 0.066 2736 Dihedral : 5.916 54.648 2136 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.59 % Allowed : 15.21 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.17), residues: 1988 helix: -0.80 (0.18), residues: 740 sheet: -2.00 (0.24), residues: 344 loop : -3.07 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 162 HIS 0.012 0.001 HIS A 219 PHE 0.035 0.003 PHE C 164 TYR 0.031 0.002 TYR D 230 ARG 0.009 0.001 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7843 (mmtp) REVERT: A 18 GLU cc_start: 0.7369 (tp30) cc_final: 0.7069 (tp30) REVERT: A 24 TRP cc_start: 0.7743 (m100) cc_final: 0.7152 (m100) REVERT: A 90 LEU cc_start: 0.8180 (mt) cc_final: 0.7657 (mp) REVERT: A 155 PHE cc_start: 0.7627 (m-80) cc_final: 0.7280 (m-80) REVERT: A 427 LYS cc_start: 0.7928 (tptt) cc_final: 0.7464 (tptt) REVERT: B 124 MET cc_start: 0.6959 (mtm) cc_final: 0.6666 (mtt) REVERT: B 158 MET cc_start: 0.5352 (mmm) cc_final: 0.5059 (mmm) REVERT: B 210 HIS cc_start: 0.5470 (OUTLIER) cc_final: 0.4681 (t-90) REVERT: B 273 LEU cc_start: 0.7767 (mp) cc_final: 0.7435 (tp) REVERT: B 359 LYS cc_start: 0.5257 (OUTLIER) cc_final: 0.3864 (tttt) REVERT: C 155 PHE cc_start: 0.8416 (m-80) cc_final: 0.8199 (m-10) REVERT: C 159 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7118 (mp) REVERT: C 238 PHE cc_start: 0.7936 (t80) cc_final: 0.7602 (t80) REVERT: D 386 ILE cc_start: 0.8536 (mt) cc_final: 0.8240 (mt) REVERT: D 498 MET cc_start: 0.3487 (OUTLIER) cc_final: 0.3069 (tmm) outliers start: 59 outliers final: 32 residues processed: 332 average time/residue: 0.2717 time to fit residues: 132.9967 Evaluate side-chains 284 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 498 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 10 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 58 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 95 GLN A 115 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 337 ASN C 78 GLN C 209 GLN C 436 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.232584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.180794 restraints weight = 18792.060| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.12 r_work: 0.3833 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15508 Z= 0.243 Angle : 0.590 7.574 21028 Z= 0.301 Chirality : 0.046 0.225 2388 Planarity : 0.005 0.064 2736 Dihedral : 5.533 53.255 2127 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.71 % Allowed : 17.21 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.18), residues: 1988 helix: -0.16 (0.19), residues: 747 sheet: -1.63 (0.25), residues: 342 loop : -2.74 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 162 HIS 0.009 0.001 HIS A 210 PHE 0.026 0.002 PHE A 164 TYR 0.025 0.002 TYR D 76 ARG 0.007 0.001 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 1.792 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: A 9 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7774 (mmtp) REVERT: A 24 TRP cc_start: 0.7776 (m100) cc_final: 0.7139 (m100) REVERT: A 90 LEU cc_start: 0.8183 (mt) cc_final: 0.7655 (mp) REVERT: A 361 TYR cc_start: 0.7658 (m-80) cc_final: 0.7339 (m-80) REVERT: A 501 MET cc_start: 0.1277 (mmt) cc_final: 0.0437 (mpp) REVERT: B 164 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.5625 (p90) REVERT: B 210 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.4850 (t-90) REVERT: B 327 ILE cc_start: 0.5461 (OUTLIER) cc_final: 0.5200 (pt) REVERT: B 359 LYS cc_start: 0.5258 (OUTLIER) cc_final: 0.3860 (tttt) REVERT: C 238 PHE cc_start: 0.7908 (t80) cc_final: 0.7589 (t80) REVERT: D 386 ILE cc_start: 0.8529 (mt) cc_final: 0.8222 (mt) REVERT: D 487 GLU cc_start: 0.3066 (OUTLIER) cc_final: -0.1977 (mp0) REVERT: D 498 MET cc_start: 0.3274 (OUTLIER) cc_final: 0.2923 (tmm) outliers start: 61 outliers final: 36 residues processed: 316 average time/residue: 0.2707 time to fit residues: 126.5267 Evaluate side-chains 289 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 498 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 314 ASN C 78 GLN C 249 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.230273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.178572 restraints weight = 18783.101| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.17 r_work: 0.3788 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15508 Z= 0.288 Angle : 0.615 9.310 21028 Z= 0.312 Chirality : 0.047 0.246 2388 Planarity : 0.005 0.064 2736 Dihedral : 5.532 57.253 2124 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.68 % Allowed : 17.82 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 1988 helix: 0.05 (0.19), residues: 745 sheet: -1.43 (0.26), residues: 344 loop : -2.56 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 162 HIS 0.008 0.001 HIS A 210 PHE 0.028 0.002 PHE A 164 TYR 0.020 0.002 TYR D 230 ARG 0.004 0.000 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 272 time to evaluate : 1.475 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: A 24 TRP cc_start: 0.7745 (m100) cc_final: 0.7138 (m100) REVERT: A 51 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7685 (tt) REVERT: A 90 LEU cc_start: 0.8153 (mt) cc_final: 0.7685 (mp) REVERT: A 128 MET cc_start: 0.3570 (tpp) cc_final: 0.2526 (ptm) REVERT: A 155 PHE cc_start: 0.7491 (m-80) cc_final: 0.7287 (m-80) REVERT: A 361 TYR cc_start: 0.7644 (m-80) cc_final: 0.7335 (m-80) REVERT: A 427 LYS cc_start: 0.7872 (tptt) cc_final: 0.7565 (tptt) REVERT: A 501 MET cc_start: 0.1616 (mmt) cc_final: 0.0591 (mpp) REVERT: B 164 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.5735 (p90) REVERT: B 188 LEU cc_start: 0.7959 (mm) cc_final: 0.7725 (mm) REVERT: B 210 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.4927 (t-90) REVERT: B 359 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.3832 (tttt) REVERT: C 238 PHE cc_start: 0.7950 (t80) cc_final: 0.7607 (t80) REVERT: D 386 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 431 LEU cc_start: 0.8121 (mp) cc_final: 0.7801 (tp) REVERT: D 487 GLU cc_start: 0.3149 (OUTLIER) cc_final: -0.1994 (mp0) REVERT: D 498 MET cc_start: 0.3341 (OUTLIER) cc_final: 0.3033 (tmm) outliers start: 77 outliers final: 49 residues processed: 330 average time/residue: 0.2777 time to fit residues: 137.2242 Evaluate side-chains 305 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 498 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 131 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 430 HIS ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.230635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178600 restraints weight = 18969.449| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.21 r_work: 0.3770 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15508 Z= 0.315 Angle : 0.632 8.349 21028 Z= 0.322 Chirality : 0.047 0.262 2388 Planarity : 0.005 0.061 2736 Dihedral : 5.656 57.480 2124 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.23 % Allowed : 19.28 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 1988 helix: 0.12 (0.19), residues: 745 sheet: -1.27 (0.26), residues: 343 loop : -2.43 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 162 HIS 0.007 0.001 HIS A 210 PHE 0.029 0.002 PHE D 227 TYR 0.022 0.002 TYR D 230 ARG 0.007 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 258 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8040 (mmtp) REVERT: A 24 TRP cc_start: 0.7802 (m100) cc_final: 0.7096 (m100) REVERT: A 90 LEU cc_start: 0.8137 (mt) cc_final: 0.7702 (mp) REVERT: A 91 ILE cc_start: 0.7319 (mm) cc_final: 0.6834 (mt) REVERT: A 128 MET cc_start: 0.3366 (tpp) cc_final: 0.2317 (ptm) REVERT: A 162 TRP cc_start: 0.8040 (m-10) cc_final: 0.7809 (m-10) REVERT: A 361 TYR cc_start: 0.7647 (m-80) cc_final: 0.7347 (m-80) REVERT: A 427 LYS cc_start: 0.7824 (tptt) cc_final: 0.7546 (tptt) REVERT: A 452 PHE cc_start: -0.0090 (OUTLIER) cc_final: -0.2419 (m-80) REVERT: A 501 MET cc_start: 0.1761 (mmt) cc_final: 0.0577 (mpp) REVERT: B 164 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.5849 (p90) REVERT: B 210 HIS cc_start: 0.5779 (OUTLIER) cc_final: 0.5029 (t-90) REVERT: B 359 LYS cc_start: 0.5149 (OUTLIER) cc_final: 0.3830 (tttt) REVERT: B 469 GLN cc_start: 0.5754 (tm-30) cc_final: 0.5225 (tm-30) REVERT: C 238 PHE cc_start: 0.7947 (t80) cc_final: 0.7580 (t80) REVERT: D 114 GLU cc_start: 0.8172 (tt0) cc_final: 0.7772 (tt0) REVERT: D 133 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5396 (tttm) REVERT: D 386 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8274 (mt) REVERT: D 487 GLU cc_start: 0.3123 (OUTLIER) cc_final: -0.1255 (mp0) outliers start: 86 outliers final: 63 residues processed: 320 average time/residue: 0.2606 time to fit residues: 125.6498 Evaluate side-chains 314 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 244 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 498 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 0.0570 chunk 144 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.228683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175966 restraints weight = 18860.429| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.12 r_work: 0.3747 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 15508 Z= 0.397 Angle : 0.674 9.310 21028 Z= 0.343 Chirality : 0.049 0.276 2388 Planarity : 0.005 0.061 2736 Dihedral : 5.834 57.258 2124 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.35 % Allowed : 19.95 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1988 helix: 0.03 (0.19), residues: 751 sheet: -1.24 (0.26), residues: 343 loop : -2.34 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 162 HIS 0.007 0.001 HIS A 210 PHE 0.034 0.002 PHE A 164 TYR 0.021 0.002 TYR D 230 ARG 0.011 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 255 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7847 (mmtp) REVERT: A 24 TRP cc_start: 0.7827 (m100) cc_final: 0.7111 (m100) REVERT: A 51 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7656 (tt) REVERT: A 91 ILE cc_start: 0.7217 (mm) cc_final: 0.6735 (mt) REVERT: A 128 MET cc_start: 0.3249 (tpp) cc_final: 0.2234 (ptm) REVERT: A 162 TRP cc_start: 0.8166 (m-10) cc_final: 0.7934 (m-10) REVERT: A 361 TYR cc_start: 0.7616 (m-80) cc_final: 0.7305 (m-80) REVERT: A 396 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 427 LYS cc_start: 0.7849 (tptt) cc_final: 0.7553 (tptt) REVERT: A 452 PHE cc_start: -0.0030 (OUTLIER) cc_final: -0.2375 (m-80) REVERT: A 501 MET cc_start: 0.1683 (mmt) cc_final: 0.0410 (mpp) REVERT: B 164 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.5859 (p90) REVERT: B 168 MET cc_start: 0.8437 (mtm) cc_final: 0.8181 (mtm) REVERT: B 210 HIS cc_start: 0.5848 (OUTLIER) cc_final: 0.5096 (t-90) REVERT: B 359 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.3865 (tttt) REVERT: B 469 GLN cc_start: 0.5658 (tm-30) cc_final: 0.5218 (tm-30) REVERT: C 238 PHE cc_start: 0.7946 (t80) cc_final: 0.7555 (t80) REVERT: D 114 GLU cc_start: 0.8207 (tt0) cc_final: 0.7893 (tt0) REVERT: D 386 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8231 (mt) REVERT: D 431 LEU cc_start: 0.7870 (mp) cc_final: 0.7570 (tp) REVERT: D 487 GLU cc_start: 0.3134 (OUTLIER) cc_final: -0.0684 (mp0) outliers start: 88 outliers final: 66 residues processed: 320 average time/residue: 0.2535 time to fit residues: 122.9907 Evaluate side-chains 316 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 484 TRP Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN C 78 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.229962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176489 restraints weight = 18961.236| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.08 r_work: 0.3802 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15508 Z= 0.220 Angle : 0.598 8.127 21028 Z= 0.303 Chirality : 0.046 0.355 2388 Planarity : 0.005 0.061 2736 Dihedral : 5.606 54.663 2124 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.56 % Allowed : 20.74 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1988 helix: 0.28 (0.19), residues: 746 sheet: -1.14 (0.26), residues: 344 loop : -2.24 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 162 HIS 0.005 0.001 HIS A 210 PHE 0.028 0.002 PHE A 164 TYR 0.021 0.001 TYR A 76 ARG 0.006 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.7851 (m100) cc_final: 0.7101 (m100) REVERT: A 91 ILE cc_start: 0.7180 (mm) cc_final: 0.6717 (mt) REVERT: A 128 MET cc_start: 0.3364 (tpp) cc_final: 0.2403 (ptm) REVERT: A 361 TYR cc_start: 0.7635 (m-80) cc_final: 0.7345 (m-80) REVERT: A 396 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8380 (p) REVERT: A 427 LYS cc_start: 0.7753 (tptt) cc_final: 0.7522 (tptt) REVERT: A 452 PHE cc_start: -0.0263 (OUTLIER) cc_final: -0.1751 (t80) REVERT: A 501 MET cc_start: 0.1599 (mmt) cc_final: 0.0439 (mpp) REVERT: B 164 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.5959 (p90) REVERT: B 210 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.5008 (t-90) REVERT: B 359 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.3850 (tttt) REVERT: B 469 GLN cc_start: 0.5607 (tm-30) cc_final: 0.4752 (tm-30) REVERT: B 471 ILE cc_start: 0.7570 (pt) cc_final: 0.7226 (pt) REVERT: B 472 GLN cc_start: 0.7215 (mm110) cc_final: 0.6944 (mp10) REVERT: B 501 MET cc_start: 0.5026 (OUTLIER) cc_final: 0.4494 (ptt) REVERT: C 138 TYR cc_start: 0.7505 (t80) cc_final: 0.7161 (t80) REVERT: C 238 PHE cc_start: 0.7935 (t80) cc_final: 0.7523 (t80) REVERT: D 114 GLU cc_start: 0.8172 (tt0) cc_final: 0.7889 (tt0) REVERT: D 218 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: D 386 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8164 (mt) REVERT: D 487 GLU cc_start: 0.3001 (OUTLIER) cc_final: -0.0921 (mp0) REVERT: D 498 MET cc_start: 0.3197 (OUTLIER) cc_final: 0.2988 (tmm) outliers start: 75 outliers final: 51 residues processed: 307 average time/residue: 0.2588 time to fit residues: 119.6525 Evaluate side-chains 302 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 498 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 77 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 49 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.227725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.174854 restraints weight = 18825.328| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.21 r_work: 0.3734 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15508 Z= 0.335 Angle : 0.663 14.810 21028 Z= 0.333 Chirality : 0.048 0.292 2388 Planarity : 0.005 0.060 2736 Dihedral : 5.679 45.359 2124 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.81 % Allowed : 20.62 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1988 helix: 0.17 (0.19), residues: 751 sheet: -1.10 (0.26), residues: 344 loop : -2.20 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 162 HIS 0.012 0.001 HIS A 219 PHE 0.031 0.002 PHE A 164 TYR 0.032 0.002 TYR D 76 ARG 0.005 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 247 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7902 (mmtp) REVERT: A 24 TRP cc_start: 0.7860 (m100) cc_final: 0.7060 (m100) REVERT: A 91 ILE cc_start: 0.6968 (mm) cc_final: 0.6557 (mt) REVERT: A 128 MET cc_start: 0.3254 (tpp) cc_final: 0.2330 (ptm) REVERT: A 162 TRP cc_start: 0.7847 (m-10) cc_final: 0.7607 (m-10) REVERT: A 361 TYR cc_start: 0.7630 (m-80) cc_final: 0.7342 (m-80) REVERT: A 427 LYS cc_start: 0.7674 (tptt) cc_final: 0.7404 (tptt) REVERT: A 452 PHE cc_start: -0.0097 (OUTLIER) cc_final: -0.2305 (m-80) REVERT: A 501 MET cc_start: 0.1632 (mmt) cc_final: 0.0318 (mpp) REVERT: B 164 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5933 (p90) REVERT: B 210 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5121 (t-90) REVERT: B 359 LYS cc_start: 0.5202 (OUTLIER) cc_final: 0.3872 (tttt) REVERT: B 443 ILE cc_start: 0.4304 (pt) cc_final: 0.3968 (pt) REVERT: B 469 GLN cc_start: 0.5489 (tm-30) cc_final: 0.5090 (tm-30) REVERT: C 138 TYR cc_start: 0.7312 (t80) cc_final: 0.6914 (t80) REVERT: C 238 PHE cc_start: 0.7895 (t80) cc_final: 0.7500 (t80) REVERT: C 288 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7776 (mt) REVERT: D 114 GLU cc_start: 0.7985 (tt0) cc_final: 0.7607 (tt0) REVERT: D 386 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8126 (mt) REVERT: D 487 GLU cc_start: 0.3185 (OUTLIER) cc_final: -0.0730 (mp0) outliers start: 79 outliers final: 59 residues processed: 307 average time/residue: 0.2514 time to fit residues: 116.9619 Evaluate side-chains 306 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.230275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177813 restraints weight = 18845.799| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.19 r_work: 0.3782 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15508 Z= 0.221 Angle : 0.614 13.322 21028 Z= 0.310 Chirality : 0.046 0.242 2388 Planarity : 0.005 0.069 2736 Dihedral : 5.440 45.631 2124 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.32 % Allowed : 21.11 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1988 helix: 0.34 (0.19), residues: 755 sheet: -1.01 (0.27), residues: 346 loop : -2.15 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 162 HIS 0.015 0.001 HIS A 219 PHE 0.028 0.002 PHE B 164 TYR 0.025 0.002 TYR A 76 ARG 0.007 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 254 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.7861 (m100) cc_final: 0.7033 (m100) REVERT: A 47 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5233 (mtp) REVERT: A 128 MET cc_start: 0.3387 (tpp) cc_final: 0.2479 (ptm) REVERT: A 361 TYR cc_start: 0.7619 (m-80) cc_final: 0.7342 (m-80) REVERT: A 427 LYS cc_start: 0.7608 (tptt) cc_final: 0.7390 (tptt) REVERT: A 452 PHE cc_start: -0.0240 (OUTLIER) cc_final: -0.1671 (t80) REVERT: A 501 MET cc_start: 0.1779 (mmt) cc_final: 0.0275 (mpp) REVERT: B 15 LYS cc_start: 0.7184 (pptt) cc_final: 0.6879 (mmmt) REVERT: B 164 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5928 (p90) REVERT: B 210 HIS cc_start: 0.5831 (OUTLIER) cc_final: 0.5102 (t-90) REVERT: B 359 LYS cc_start: 0.5132 (OUTLIER) cc_final: 0.3858 (tttt) REVERT: B 443 ILE cc_start: 0.4385 (pt) cc_final: 0.4055 (pt) REVERT: B 469 GLN cc_start: 0.5341 (tm-30) cc_final: 0.4573 (tm-30) REVERT: B 471 ILE cc_start: 0.7396 (pt) cc_final: 0.7042 (pt) REVERT: B 472 GLN cc_start: 0.7139 (mm110) cc_final: 0.6841 (mp10) REVERT: C 138 TYR cc_start: 0.7362 (t80) cc_final: 0.6982 (t80) REVERT: C 238 PHE cc_start: 0.7890 (t80) cc_final: 0.7452 (t80) REVERT: D 114 GLU cc_start: 0.7939 (tt0) cc_final: 0.7560 (tt0) REVERT: D 386 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8174 (mt) REVERT: D 487 GLU cc_start: 0.3066 (OUTLIER) cc_final: -0.0927 (mp0) outliers start: 71 outliers final: 53 residues processed: 307 average time/residue: 0.2563 time to fit residues: 118.7626 Evaluate side-chains 299 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 484 TRP Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 337 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.231854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180111 restraints weight = 18947.631| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.03 r_work: 0.3826 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15508 Z= 0.189 Angle : 0.603 8.362 21028 Z= 0.306 Chirality : 0.045 0.234 2388 Planarity : 0.005 0.070 2736 Dihedral : 5.239 46.002 2124 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.65 % Allowed : 22.32 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.19), residues: 1988 helix: 0.40 (0.19), residues: 771 sheet: -0.87 (0.27), residues: 346 loop : -2.08 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 162 HIS 0.014 0.001 HIS A 219 PHE 0.028 0.002 PHE A 164 TYR 0.017 0.001 TYR A 466 ARG 0.007 0.000 ARG B 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.7892 (m100) cc_final: 0.7058 (m100) REVERT: A 47 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5295 (mtp) REVERT: A 81 LYS cc_start: 0.8041 (mttt) cc_final: 0.7462 (mttt) REVERT: A 128 MET cc_start: 0.3382 (tpp) cc_final: 0.2387 (ptm) REVERT: A 336 CYS cc_start: 0.8480 (m) cc_final: 0.8137 (m) REVERT: A 361 TYR cc_start: 0.7604 (m-80) cc_final: 0.7344 (m-80) REVERT: A 501 MET cc_start: 0.1589 (mmt) cc_final: 0.0255 (mpp) REVERT: B 92 THR cc_start: 0.7508 (t) cc_final: 0.7295 (t) REVERT: B 210 HIS cc_start: 0.5833 (OUTLIER) cc_final: 0.5116 (t-90) REVERT: B 359 LYS cc_start: 0.5071 (OUTLIER) cc_final: 0.3780 (tttt) REVERT: B 443 ILE cc_start: 0.4361 (pt) cc_final: 0.4027 (pt) REVERT: B 469 GLN cc_start: 0.5466 (tm-30) cc_final: 0.4753 (tm-30) REVERT: C 138 TYR cc_start: 0.7609 (t80) cc_final: 0.7256 (t80) REVERT: C 238 PHE cc_start: 0.7922 (t80) cc_final: 0.7422 (t80) REVERT: C 288 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7868 (mt) REVERT: D 153 PHE cc_start: 0.7122 (p90) cc_final: 0.6908 (p90) REVERT: D 162 TRP cc_start: 0.8310 (m100) cc_final: 0.8087 (m100) REVERT: D 386 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8287 (mt) REVERT: D 487 GLU cc_start: 0.2999 (OUTLIER) cc_final: -0.2069 (mp0) outliers start: 60 outliers final: 49 residues processed: 303 average time/residue: 0.2634 time to fit residues: 119.8546 Evaluate side-chains 297 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Chi-restraints excluded: chain D residue 487 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 154 ASN C 268 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.234423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.183138 restraints weight = 18814.310| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.07 r_work: 0.3843 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15508 Z= 0.183 Angle : 0.609 14.769 21028 Z= 0.306 Chirality : 0.045 0.232 2388 Planarity : 0.005 0.067 2736 Dihedral : 5.111 45.869 2123 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.65 % Allowed : 22.57 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.19), residues: 1988 helix: 0.53 (0.19), residues: 759 sheet: -0.76 (0.28), residues: 337 loop : -2.08 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 162 HIS 0.012 0.001 HIS A 219 PHE 0.033 0.002 PHE D 215 TYR 0.026 0.001 TYR A 76 ARG 0.008 0.000 ARG C 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10076.30 seconds wall clock time: 179 minutes 1.33 seconds (10741.33 seconds total)