Starting phenix.real_space_refine on Thu Sep 18 07:17:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izw_61044/09_2025/9izw_61044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izw_61044/09_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_61044/09_2025/9izw_61044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izw_61044/09_2025/9izw_61044.map" model { file = "/net/cci-nas-00/data/ceres_data/9izw_61044/09_2025/9izw_61044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izw_61044/09_2025/9izw_61044.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.082 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.13, per 1000 atoms: 0.27 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: 1.31 Conformation dependent library (CDL) restraints added in 866.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.64 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: 3.41 Time building geometry restraints manager: 1.83 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: 0.02 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- 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= 0.165 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 240 TYR 0.040 0.001 TYR D 230 PHE 0.012 0.001 PHE A 164 TRP 0.007 0.000 TRP B 162 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00264 (15508) covalent geometry : angle 0.53455 (21028) hydrogen bonds : bond 0.17474 ( 560) hydrogen bonds : angle 6.24156 ( 1599) *********************** 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 : 0.432 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: 0.5702 (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: 0.7707 (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: 0.5968 (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: 0.7036 (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: -0.0854 (mp0) outliers start: 22 outliers final: 8 residues processed: 413 average time/residue: 0.1280 time to fit residues: 77.2364 Evaluate side-chains 297 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 285 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 337 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4623 r_free = 0.4623 target = 0.234122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.183751 restraints weight = 18861.397| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.31 r_work: 0.3794 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15508 Z= 0.237 Angle : 0.691 9.091 21028 Z= 0.354 Chirality : 0.049 0.266 2388 Planarity : 0.005 0.066 2736 Dihedral : 5.800 55.527 2136 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.47 % Allowed : 15.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.17), residues: 1988 helix: -0.69 (0.18), residues: 739 sheet: -1.99 (0.24), residues: 347 loop : -3.04 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 69 TYR 0.031 0.002 TYR D 230 PHE 0.035 0.002 PHE C 164 TRP 0.023 0.003 TRP D 162 HIS 0.011 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00565 (15508) covalent geometry : angle 0.69146 (21028) hydrogen bonds : bond 0.04150 ( 560) hydrogen bonds : angle 4.76631 ( 1599) *********************** 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 349 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 292 time to evaluate : 0.542 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 24 TRP cc_start: 0.7738 (m100) cc_final: 0.7068 (m100) REVERT: A 361 TYR cc_start: 0.7582 (m-80) cc_final: 0.7313 (m-80) REVERT: B 47 MET cc_start: 0.5127 (mmm) cc_final: 0.4842 (mmm) REVERT: B 158 MET cc_start: 0.5359 (mmm) cc_final: 0.5044 (mmm) REVERT: B 210 HIS cc_start: 0.5421 (OUTLIER) cc_final: 0.4666 (t-90) REVERT: B 359 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.3834 (tttt) REVERT: C 238 PHE cc_start: 0.7813 (t80) cc_final: 0.7484 (t80) REVERT: D 386 ILE cc_start: 0.8433 (mt) cc_final: 0.8228 (mt) REVERT: D 498 MET cc_start: 0.3214 (OUTLIER) cc_final: 0.2783 (tmm) outliers start: 57 outliers final: 27 residues processed: 334 average time/residue: 0.1184 time to fit residues: 58.7795 Evaluate side-chains 278 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 169 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 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 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 323 LEU Chi-restraints excluded: chain D residue 441 VAL 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 190 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** 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 314 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** D 413 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.231274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.180022 restraints weight = 19021.129| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.23 r_work: 0.3753 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 15508 Z= 0.229 Angle : 0.669 16.530 21028 Z= 0.337 Chirality : 0.048 0.252 2388 Planarity : 0.005 0.062 2736 Dihedral : 5.525 54.456 2120 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.01 % Allowed : 16.67 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.18), residues: 1988 helix: -0.30 (0.18), residues: 746 sheet: -1.75 (0.25), residues: 346 loop : -2.77 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 181 TYR 0.029 0.002 TYR D 230 PHE 0.032 0.002 PHE A 164 TRP 0.018 0.002 TRP D 162 HIS 0.009 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00553 (15508) covalent geometry : angle 0.66863 (21028) hydrogen bonds : bond 0.03866 ( 560) hydrogen bonds : angle 4.58720 ( 1599) *********************** 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 320 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 0.497 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 24 TRP cc_start: 0.7765 (m100) cc_final: 0.7069 (m100) REVERT: A 128 MET cc_start: 0.3343 (tpp) cc_final: 0.3031 (tpp) REVERT: A 162 TRP cc_start: 0.7910 (m-10) cc_final: 0.7688 (m-10) REVERT: A 361 TYR cc_start: 0.7707 (m-80) cc_final: 0.7417 (m-80) REVERT: A 427 LYS cc_start: 0.7713 (tptt) cc_final: 0.7402 (tptt) REVERT: A 501 MET cc_start: 0.1253 (mmt) cc_final: 0.0291 (mpp) REVERT: B 47 MET cc_start: 0.5113 (mmm) cc_final: 0.4906 (mmm) REVERT: B 164 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.5585 (p90) REVERT: B 210 HIS cc_start: 0.5608 (OUTLIER) cc_final: 0.4850 (t-90) REVERT: B 359 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.3883 (tttt) REVERT: C 238 PHE cc_start: 0.7892 (t80) cc_final: 0.7584 (t80) REVERT: D 386 ILE cc_start: 0.8462 (mt) cc_final: 0.8197 (mt) REVERT: D 487 GLU cc_start: 0.3126 (OUTLIER) cc_final: -0.1887 (mp0) outliers start: 66 outliers final: 40 residues processed: 307 average time/residue: 0.1157 time to fit residues: 53.5838 Evaluate side-chains 281 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 127 THR 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 437 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 7 THR 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 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 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 441 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 249 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4610 r_free = 0.4610 target = 0.232554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.180664 restraints weight = 18818.633| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.07 r_work: 0.3776 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15508 Z= 0.158 Angle : 0.604 12.069 21028 Z= 0.305 Chirality : 0.046 0.227 2388 Planarity : 0.005 0.061 2736 Dihedral : 5.451 57.441 2120 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.26 % Allowed : 18.49 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.18), residues: 1988 helix: 0.00 (0.19), residues: 748 sheet: -1.45 (0.26), residues: 344 loop : -2.53 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.019 0.001 TYR D 230 PHE 0.028 0.002 PHE A 164 TRP 0.020 0.001 TRP D 162 HIS 0.013 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00384 (15508) covalent geometry : angle 0.60383 (21028) hydrogen bonds : bond 0.03337 ( 560) hydrogen bonds : angle 4.40754 ( 1599) *********************** 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 335 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 0.522 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: 0.7785 (m100) cc_final: 0.7120 (m100) REVERT: A 51 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 128 MET cc_start: 0.3434 (tpp) cc_final: 0.2430 (ptm) REVERT: A 155 PHE cc_start: 0.7535 (m-80) cc_final: 0.7180 (m-80) REVERT: A 286 MET cc_start: 0.8148 (mmm) cc_final: 0.7885 (mtt) REVERT: A 361 TYR cc_start: 0.7716 (m-80) cc_final: 0.7393 (m-80) REVERT: A 501 MET cc_start: 0.1408 (mmt) cc_final: 0.0312 (mpp) REVERT: B 164 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.5669 (p90) REVERT: B 210 HIS cc_start: 0.5555 (OUTLIER) cc_final: 0.4821 (t-90) REVERT: B 359 LYS cc_start: 0.5211 (OUTLIER) cc_final: 0.3853 (tttt) REVERT: C 124 MET cc_start: 0.6888 (ttt) cc_final: 0.6574 (tmm) REVERT: C 238 PHE cc_start: 0.7933 (t80) cc_final: 0.7574 (t80) REVERT: D 386 ILE cc_start: 0.8526 (mt) cc_final: 0.8244 (mt) REVERT: D 487 GLU cc_start: 0.2977 (OUTLIER) cc_final: -0.2088 (mp0) REVERT: D 498 MET cc_start: 0.3327 (OUTLIER) cc_final: 0.3040 (tmm) outliers start: 70 outliers final: 45 residues processed: 319 average time/residue: 0.1210 time to fit residues: 57.9691 Evaluate side-chains 295 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 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 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 THR 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 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 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 D residue 64 THR 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 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 381 CYS 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 27 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 74 optimal weight: 40.0000 chunk 55 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 256 ASN A 271 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 256 ASN B 430 HIS C 78 GLN C 209 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.231231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.178938 restraints weight = 18807.958| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.20 r_work: 0.3804 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15508 Z= 0.146 Angle : 0.597 12.515 21028 Z= 0.300 Chirality : 0.045 0.229 2388 Planarity : 0.005 0.060 2736 Dihedral : 5.383 57.058 2120 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.11 % Allowed : 18.86 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.19), residues: 1988 helix: 0.25 (0.19), residues: 749 sheet: -1.29 (0.26), residues: 342 loop : -2.38 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 181 TYR 0.019 0.001 TYR D 230 PHE 0.027 0.002 PHE A 164 TRP 0.021 0.001 TRP D 162 HIS 0.012 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00355 (15508) covalent geometry : angle 0.59705 (21028) hydrogen bonds : bond 0.03158 ( 560) hydrogen bonds : angle 4.31731 ( 1599) *********************** 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 345 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 261 time to evaluate : 0.585 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: 0.8245 (mmtm) cc_final: 0.8000 (mmtp) REVERT: A 24 TRP cc_start: 0.7804 (m100) cc_final: 0.7117 (m100) REVERT: A 82 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 91 ILE cc_start: 0.7291 (mm) cc_final: 0.6820 (mt) REVERT: A 128 MET cc_start: 0.3593 (tpp) cc_final: 0.2489 (ptm) REVERT: A 286 MET cc_start: 0.7999 (mmm) cc_final: 0.7707 (mtt) REVERT: A 361 TYR cc_start: 0.7626 (m-80) cc_final: 0.7340 (m-80) REVERT: A 501 MET cc_start: 0.1788 (mmt) cc_final: 0.0591 (mpp) REVERT: B 164 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.5693 (p90) REVERT: B 210 HIS cc_start: 0.5719 (OUTLIER) cc_final: 0.4935 (t-90) REVERT: B 327 ILE cc_start: 0.5591 (OUTLIER) cc_final: 0.4902 (tt) REVERT: B 359 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.3792 (tttt) REVERT: B 469 GLN cc_start: 0.5728 (tm-30) cc_final: 0.5252 (tm-30) REVERT: B 471 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7434 (pt) REVERT: C 238 PHE cc_start: 0.7865 (t80) cc_final: 0.7549 (t80) REVERT: C 472 GLN cc_start: 0.8416 (tt0) cc_final: 0.8006 (mt0) REVERT: D 133 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5389 (tttm) REVERT: D 386 ILE cc_start: 0.8583 (mt) cc_final: 0.8276 (mt) REVERT: D 487 GLU cc_start: 0.3151 (OUTLIER) cc_final: -0.1975 (mp0) REVERT: D 498 MET cc_start: 0.3332 (OUTLIER) cc_final: 0.3070 (tmm) outliers start: 84 outliers final: 56 residues processed: 322 average time/residue: 0.1199 time to fit residues: 58.5981 Evaluate side-chains 306 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 119 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 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 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 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 471 ILE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 MET 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 404 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 126 GLU 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 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 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 381 CYS 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 3 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 146 optimal weight: 0.0370 overall best weight: 3.0064 ------------------------------------------------------------------------------- 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 256 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 207 HIS ** 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 = 0.4564 r_free = 0.4564 target = 0.227930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176507 restraints weight = 18853.619| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.16 r_work: 0.3759 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15508 Z= 0.226 Angle : 0.667 12.164 21028 Z= 0.336 Chirality : 0.048 0.274 2388 Planarity : 0.005 0.059 2736 Dihedral : 5.615 55.599 2120 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.93 % Allowed : 19.65 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.19), residues: 1988 helix: 0.08 (0.19), residues: 753 sheet: -1.30 (0.26), residues: 344 loop : -2.32 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 354 TYR 0.022 0.002 TYR D 230 PHE 0.034 0.002 PHE A 164 TRP 0.022 0.002 TRP D 162 HIS 0.013 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00550 (15508) covalent geometry : angle 0.66698 (21028) hydrogen bonds : bond 0.03656 ( 560) hydrogen bonds : angle 4.51745 ( 1599) *********************** 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 333 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7916 (mmtp) REVERT: A 24 TRP cc_start: 0.7817 (m100) cc_final: 0.7085 (m100) REVERT: A 51 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7620 (tt) REVERT: A 91 ILE cc_start: 0.7102 (mm) cc_final: 0.6672 (mt) REVERT: A 128 MET cc_start: 0.3477 (tpp) cc_final: 0.2418 (ptm) REVERT: A 361 TYR cc_start: 0.7592 (m-80) cc_final: 0.7287 (m-80) REVERT: A 452 PHE cc_start: 0.0053 (OUTLIER) cc_final: -0.2270 (m-80) REVERT: A 501 MET cc_start: 0.1744 (mmt) cc_final: 0.0422 (mpp) REVERT: B 164 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5732 (p90) REVERT: B 168 MET cc_start: 0.8358 (mtm) cc_final: 0.8121 (mtm) REVERT: B 210 HIS cc_start: 0.5888 (OUTLIER) cc_final: 0.5132 (t-90) REVERT: B 359 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.3842 (tttt) REVERT: B 469 GLN cc_start: 0.5582 (tm-30) cc_final: 0.5141 (tm-30) REVERT: B 498 MET cc_start: 0.2990 (ptp) cc_final: 0.2613 (ptp) REVERT: C 238 PHE cc_start: 0.7871 (t80) cc_final: 0.7521 (t80) REVERT: D 114 GLU cc_start: 0.7983 (tt0) cc_final: 0.7679 (tt0) REVERT: D 386 ILE cc_start: 0.8603 (mt) cc_final: 0.8351 (mt) REVERT: D 431 LEU cc_start: 0.8055 (mp) cc_final: 0.7726 (tp) REVERT: D 487 GLU cc_start: 0.3453 (OUTLIER) cc_final: -0.1633 (mp0) outliers start: 81 outliers final: 65 residues processed: 313 average time/residue: 0.1091 time to fit residues: 53.2436 Evaluate side-chains 310 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 66 VAL 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 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 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 205 ILE 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 404 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 484 TRP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 126 GLU 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 343 THR Chi-restraints excluded: chain D residue 378 ASN 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 6 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- 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 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN C 78 GLN C 337 ASN ** 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 = 0.4570 r_free = 0.4570 target = 0.227951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175328 restraints weight = 18681.334| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.15 r_work: 0.3752 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 15508 Z= 0.264 Angle : 0.705 13.121 21028 Z= 0.355 Chirality : 0.050 0.275 2388 Planarity : 0.005 0.059 2736 Dihedral : 5.815 54.135 2120 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 5.05 % Allowed : 19.77 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.19), residues: 1988 helix: -0.10 (0.19), residues: 765 sheet: -1.20 (0.27), residues: 340 loop : -2.28 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 354 TYR 0.021 0.002 TYR D 230 PHE 0.031 0.002 PHE D 164 TRP 0.025 0.002 TRP D 162 HIS 0.014 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00644 (15508) covalent geometry : angle 0.70469 (21028) hydrogen bonds : bond 0.03857 ( 560) hydrogen bonds : angle 4.65600 ( 1599) *********************** 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 324 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 241 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7983 (mmtp) REVERT: A 24 TRP cc_start: 0.7872 (m100) cc_final: 0.7094 (m100) REVERT: A 91 ILE cc_start: 0.7278 (mm) cc_final: 0.6874 (mt) REVERT: A 128 MET cc_start: 0.3514 (tpp) cc_final: 0.2426 (ptm) REVERT: A 361 TYR cc_start: 0.7616 (m-80) cc_final: 0.7325 (m-80) REVERT: A 452 PHE cc_start: 0.0067 (OUTLIER) cc_final: -0.2252 (m-80) REVERT: A 501 MET cc_start: 0.1836 (mmt) cc_final: 0.0493 (mpp) REVERT: B 164 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6084 (p90) REVERT: B 210 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5151 (t-90) REVERT: B 359 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.3849 (tttt) REVERT: B 469 GLN cc_start: 0.5881 (tm-30) cc_final: 0.5416 (tm-30) REVERT: C 238 PHE cc_start: 0.7959 (t80) cc_final: 0.7569 (t80) REVERT: D 114 GLU cc_start: 0.8167 (tt0) cc_final: 0.7896 (tt0) REVERT: D 386 ILE cc_start: 0.8598 (mt) cc_final: 0.8268 (mt) REVERT: D 431 LEU cc_start: 0.8099 (mp) cc_final: 0.7741 (tp) REVERT: D 487 GLU cc_start: 0.3544 (OUTLIER) cc_final: -0.1539 (mp0) outliers start: 83 outliers final: 63 residues processed: 304 average time/residue: 0.1094 time to fit residues: 51.6648 Evaluate side-chains 303 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 66 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 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 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 137 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 205 ILE 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 182 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 404 GLN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 484 TRP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 126 GLU 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 343 THR Chi-restraints excluded: chain D residue 378 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 119 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4587 r_free = 0.4587 target = 0.230297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.178441 restraints weight = 18981.685| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.16 r_work: 0.3829 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15508 Z= 0.128 Angle : 0.612 11.969 21028 Z= 0.307 Chirality : 0.045 0.247 2388 Planarity : 0.005 0.060 2736 Dihedral : 5.394 45.526 2120 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.08 % Allowed : 21.11 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.19), residues: 1988 helix: 0.28 (0.19), residues: 750 sheet: -1.18 (0.27), residues: 342 loop : -2.17 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 56 TYR 0.030 0.001 TYR D 76 PHE 0.027 0.002 PHE B 164 TRP 0.029 0.001 TRP D 162 HIS 0.012 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00308 (15508) covalent geometry : angle 0.61163 (21028) hydrogen bonds : bond 0.03076 ( 560) hydrogen bonds : angle 4.35508 ( 1599) *********************** 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 319 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.7881 (m100) cc_final: 0.7117 (m100) REVERT: A 91 ILE cc_start: 0.7234 (mm) cc_final: 0.6847 (mt) REVERT: A 128 MET cc_start: 0.3507 (tpp) cc_final: 0.2501 (ptm) REVERT: A 361 TYR cc_start: 0.7584 (m-80) cc_final: 0.7313 (m-80) REVERT: A 413 ASN cc_start: 0.7788 (p0) cc_final: 0.7239 (t0) REVERT: A 452 PHE cc_start: 0.0001 (OUTLIER) cc_final: -0.2356 (m-80) REVERT: A 501 MET cc_start: 0.1823 (mmt) cc_final: 0.0529 (mpp) REVERT: B 24 TRP cc_start: 0.6400 (m100) cc_final: 0.5926 (m100) REVERT: B 164 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6056 (p90) REVERT: B 210 HIS cc_start: 0.5856 (OUTLIER) cc_final: 0.5121 (t-90) REVERT: B 327 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.4994 (tt) REVERT: B 359 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.3811 (tttt) REVERT: B 469 GLN cc_start: 0.5718 (tm-30) cc_final: 0.4915 (tm-30) REVERT: B 472 GLN cc_start: 0.7183 (mm110) cc_final: 0.6936 (mp10) REVERT: C 138 TYR cc_start: 0.7582 (t80) cc_final: 0.7235 (t80) REVERT: C 238 PHE cc_start: 0.7940 (t80) cc_final: 0.7487 (t80) REVERT: D 114 GLU cc_start: 0.8136 (tt0) cc_final: 0.7877 (tt0) REVERT: D 386 ILE cc_start: 0.8583 (mt) cc_final: 0.8257 (mt) REVERT: D 487 GLU cc_start: 0.3226 (OUTLIER) cc_final: -0.0943 (mp0) REVERT: D 498 MET cc_start: 0.3204 (tmm) cc_final: 0.2990 (tmm) outliers start: 67 outliers final: 47 residues processed: 304 average time/residue: 0.1147 time to fit residues: 53.4297 Evaluate side-chains 290 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 131 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 447 LEU 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 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 205 ILE 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 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 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 479 THR 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 169 VAL 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 343 THR Chi-restraints excluded: chain D residue 378 ASN 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 67 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 12 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 48 optimal weight: 5.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN C 209 GLN C 440 ASN D 41 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 = 0.4615 r_free = 0.4615 target = 0.233089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.178161 restraints weight = 18791.623| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.34 r_work: 0.3859 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15508 Z= 0.108 Angle : 0.603 15.345 21028 Z= 0.300 Chirality : 0.045 0.231 2388 Planarity : 0.004 0.059 2736 Dihedral : 5.112 45.771 2120 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.65 % Allowed : 21.72 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.19), residues: 1988 helix: 0.44 (0.19), residues: 756 sheet: -0.95 (0.27), residues: 350 loop : -2.07 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 56 TYR 0.019 0.001 TYR D 230 PHE 0.027 0.002 PHE B 164 TRP 0.033 0.001 TRP D 162 HIS 0.014 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00256 (15508) covalent geometry : angle 0.60284 (21028) hydrogen bonds : bond 0.02896 ( 560) hydrogen bonds : angle 4.24521 ( 1599) *********************** 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 313 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.627 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: 0.7879 (m100) cc_final: 0.7111 (m100) REVERT: A 47 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5195 (mtp) REVERT: A 81 LYS cc_start: 0.8035 (mttt) cc_final: 0.7459 (mttt) REVERT: A 128 MET cc_start: 0.3346 (tpp) cc_final: 0.2404 (ptm) REVERT: A 336 CYS cc_start: 0.8435 (m) cc_final: 0.8089 (m) REVERT: A 361 TYR cc_start: 0.7574 (m-80) cc_final: 0.7311 (m-80) REVERT: A 413 ASN cc_start: 0.7659 (p0) cc_final: 0.7202 (t0) REVERT: A 452 PHE cc_start: -0.0224 (OUTLIER) cc_final: -0.2437 (m-80) REVERT: A 501 MET cc_start: 0.1669 (mmt) cc_final: 0.0450 (mpp) REVERT: B 24 TRP cc_start: 0.6298 (m100) cc_final: 0.5842 (m100) REVERT: B 164 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5876 (p90) REVERT: B 210 HIS cc_start: 0.5787 (OUTLIER) cc_final: 0.5059 (t-90) REVERT: B 359 LYS cc_start: 0.5063 (OUTLIER) cc_final: 0.3787 (tttt) REVERT: B 469 GLN cc_start: 0.5546 (tm-30) cc_final: 0.4737 (tm-30) REVERT: B 471 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7001 (pt) REVERT: B 472 GLN cc_start: 0.7026 (mm110) cc_final: 0.6731 (mp10) REVERT: B 498 MET cc_start: 0.3133 (ptp) cc_final: 0.2698 (ptp) REVERT: C 124 MET cc_start: 0.6854 (tmm) cc_final: 0.6497 (tmm) REVERT: C 138 TYR cc_start: 0.7549 (t80) cc_final: 0.7162 (t80) REVERT: C 238 PHE cc_start: 0.7883 (t80) cc_final: 0.7361 (t80) REVERT: D 126 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: D 386 ILE cc_start: 0.8586 (mt) cc_final: 0.8239 (mt) outliers start: 60 outliers final: 41 residues processed: 296 average time/residue: 0.1142 time to fit residues: 51.7648 Evaluate side-chains 283 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 252 MET 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 447 LEU 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 164 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 205 ILE 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 359 LYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 471 ILE 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 51 ILE 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 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 169 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 57 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 95 optimal weight: 0.0470 overall best weight: 4.4086 ------------------------------------------------------------------------------- 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 436 GLN B 70 GLN C 78 GLN C 440 ASN ** 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 = 0.4565 r_free = 0.4565 target = 0.226960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174474 restraints weight = 18894.324| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.26 r_work: 0.3697 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 15508 Z= 0.310 Angle : 0.769 11.767 21028 Z= 0.388 Chirality : 0.052 0.310 2388 Planarity : 0.005 0.057 2736 Dihedral : 5.698 44.856 2119 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.53 % Allowed : 22.32 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.19), residues: 1988 helix: -0.03 (0.19), residues: 758 sheet: -0.98 (0.28), residues: 336 loop : -2.22 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 56 TYR 0.031 0.002 TYR A 76 PHE 0.038 0.003 PHE D 164 TRP 0.046 0.003 TRP D 162 HIS 0.014 0.002 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00754 (15508) covalent geometry : angle 0.76882 (21028) hydrogen bonds : bond 0.04076 ( 560) hydrogen bonds : angle 4.77169 ( 1599) ********************** 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 295 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.7914 (m100) cc_final: 0.7050 (m100) REVERT: A 47 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5344 (mtp) REVERT: A 81 LYS cc_start: 0.8187 (mttt) cc_final: 0.7549 (mttt) REVERT: A 128 MET cc_start: 0.3160 (tpp) cc_final: 0.2315 (ptm) REVERT: A 361 TYR cc_start: 0.7658 (m-80) cc_final: 0.7280 (m-80) REVERT: A 452 PHE cc_start: 0.0190 (OUTLIER) cc_final: -0.2094 (m-80) REVERT: A 501 MET cc_start: 0.1684 (mmt) cc_final: 0.0345 (mpp) REVERT: B 138 TYR cc_start: 0.7651 (p90) cc_final: 0.6827 (p90) REVERT: B 163 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8046 (mtt) REVERT: B 210 HIS cc_start: 0.5814 (OUTLIER) cc_final: 0.5137 (t-90) REVERT: B 359 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.3670 (ttpt) REVERT: B 469 GLN cc_start: 0.5651 (tm-30) cc_final: 0.5194 (tm-30) REVERT: C 128 MET cc_start: 0.3923 (ttp) cc_final: 0.3683 (ptp) REVERT: C 138 TYR cc_start: 0.7309 (t80) cc_final: 0.6921 (t80) REVERT: C 238 PHE cc_start: 0.7942 (t80) cc_final: 0.7623 (t80) REVERT: D 11 PHE cc_start: 0.6991 (t80) cc_final: 0.6599 (t80) REVERT: D 114 GLU cc_start: 0.7991 (tt0) cc_final: 0.7741 (tt0) REVERT: D 386 ILE cc_start: 0.8611 (mt) cc_final: 0.8294 (mt) outliers start: 58 outliers final: 48 residues processed: 282 average time/residue: 0.1097 time to fit residues: 48.0435 Evaluate side-chains 280 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ILE 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 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 163 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 205 ILE 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 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 51 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 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 479 THR Chi-restraints excluded: chain C residue 484 TRP 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 169 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 12 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 219 HIS ** 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 = 0.4610 r_free = 0.4610 target = 0.232017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180260 restraints weight = 18706.673| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.09 r_work: 0.3803 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15508 Z= 0.131 Angle : 0.638 11.655 21028 Z= 0.321 Chirality : 0.046 0.239 2388 Planarity : 0.005 0.059 2736 Dihedral : 5.358 45.546 2119 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.28 % Allowed : 22.99 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.19), residues: 1988 helix: 0.24 (0.19), residues: 760 sheet: -0.96 (0.28), residues: 339 loop : -2.11 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 56 TYR 0.029 0.001 TYR A 76 PHE 0.027 0.002 PHE A 164 TRP 0.028 0.001 TRP D 162 HIS 0.015 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00316 (15508) covalent geometry : angle 0.63801 (21028) hydrogen bonds : bond 0.03078 ( 560) hydrogen bonds : angle 4.43423 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5014.55 seconds wall clock time: 86 minutes 41.41 seconds (5201.41 seconds total)