Starting phenix.real_space_refine on Thu Jun 12 11:57:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izv_61043/06_2025/9izv_61043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izv_61043/06_2025/9izv_61043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izv_61043/06_2025/9izv_61043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izv_61043/06_2025/9izv_61043.map" model { file = "/net/cci-nas-00/data/ceres_data/9izv_61043/06_2025/9izv_61043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izv_61043/06_2025/9izv_61043.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.044 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 91 5.16 5 C 8961 2.51 5 N 2445 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3695 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 27, 'TRANS': 457} Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3320 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 26, 'TRANS': 412} Chain breaks: 2 Chain: "C" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3580 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 27, 'TRANS': 442} Chain breaks: 1 Chain: "D" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3523 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 26, 'TRANS': 436} Chain breaks: 2 Time building chain proxies: 8.33, per 1000 atoms: 0.59 Number of scatterers: 14118 At special positions: 0 Unit cell: (111.24, 119.48, 115.36, 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 91 16.00 O 2621 8.00 N 2445 7.00 C 8961 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: 3.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 48.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 43 through 64 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 98 through 118 removed outlier: 3.544A pdb=" N SER A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 157 through 170 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.542A pdb=" N THR A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.541A pdb=" N ARG A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.091A pdb=" N LYS A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.686A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.996A pdb=" N LYS A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'B' and resid 43 through 64 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 83 through 96 Processing helix chain 'B' and resid 98 through 118 Processing helix chain 'B' and resid 158 through 171 Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.411A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 296 through 299 removed outlier: 3.545A pdb=" N LYS B 299 " --> pdb=" O GLU B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 328 through 345 Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.750A pdb=" N ASN B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 468 through 475 removed outlier: 4.346A pdb=" N GLN B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 64 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 65 through 83 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 98 through 118 removed outlier: 3.690A pdb=" N SER C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.570A pdb=" N MET C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 170 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.693A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 265 through 278 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 296 through 310 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 328 through 345 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'D' and resid 43 through 64 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 98 through 119 removed outlier: 3.574A pdb=" N VAL D 119 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.082A pdb=" N MET D 123 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.684A pdb=" N THR D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.677A pdb=" N HIS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 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 311 removed outlier: 3.536A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 345 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 398 through 409 removed outlier: 3.566A pdb=" N ASN D 409 " --> pdb=" O ILE D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 467 through 475 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 349 through 351 removed outlier: 3.741A pdb=" N LEU B 351 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS B 257 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR A 479 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 439 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR A 481 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 127 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU C 126 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG C 141 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET C 128 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N SER C 139 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 130 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU C 137 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL D 437 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR C 479 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL D 439 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C 481 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR D 415 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS D 257 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY D 258 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 294 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL D 260 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 396 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU D 391 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR D 370 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 393 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 372 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLU D 395 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY D 353 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR D 370 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 351 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 372 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 349 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.638A pdb=" N CYS A 147 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LYS A 177 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY A 149 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 146 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 224 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 229 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351 removed outlier: 6.451A pdb=" N ILE A 371 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 370 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL A 393 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 372 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU A 395 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 293 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 294 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS A 257 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE A 418 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 259 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 415 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.622A pdb=" N GLY B 37 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.489A pdb=" N PHE B 174 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS B 147 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS B 177 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY B 149 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 146 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA B 224 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS B 223 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 28 Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 205 removed outlier: 7.505A pdb=" N VAL C 146 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 225 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 148 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE C 227 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 150 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 251 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 349 through 351 removed outlier: 5.853A pdb=" N ILE C 349 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER C 373 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 351 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU C 395 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C 258 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 294 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 260 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 415 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 437 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 24 through 28 removed outlier: 3.652A pdb=" N GLY D 37 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.887A pdb=" N VAL D 146 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 224 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 228 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS D 223 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLN D 249 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 225 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASN D 251 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE D 227 " --> pdb=" O ASN D 251 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3695 1.33 - 1.45: 2290 1.45 - 1.57: 8263 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14398 Sorted by residual: bond pdb=" N ARG A 456 " pdb=" CA ARG A 456 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.09e-02 8.42e+03 5.28e+00 bond pdb=" N SER A 457 " pdb=" CA SER A 457 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.27e-02 6.20e+03 5.09e+00 bond pdb=" C ARG A 456 " pdb=" O ARG A 456 " ideal model delta sigma weight residual 1.234 1.214 0.020 1.00e-02 1.00e+04 4.04e+00 bond pdb=" N SER A 455 " pdb=" CA SER A 455 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.88e+00 bond pdb=" CA SER A 458 " pdb=" C SER A 458 " ideal model delta sigma weight residual 1.522 1.549 -0.027 1.43e-02 4.89e+03 3.70e+00 ... (remaining 14393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 19362 2.34 - 4.69: 142 4.69 - 7.03: 5 7.03 - 9.37: 1 9.37 - 11.71: 1 Bond angle restraints: 19511 Sorted by residual: angle pdb=" N SER A 455 " pdb=" CA SER A 455 " pdb=" C SER A 455 " ideal model delta sigma weight residual 110.80 122.51 -11.71 2.13e+00 2.20e-01 3.02e+01 angle pdb=" N VAL B 375 " pdb=" CA VAL B 375 " pdb=" C VAL B 375 " ideal model delta sigma weight residual 109.12 100.85 8.27 1.58e+00 4.01e-01 2.74e+01 angle pdb=" N SER A 458 " pdb=" CA SER A 458 " pdb=" C SER A 458 " ideal model delta sigma weight residual 112.87 116.90 -4.03 1.20e+00 6.94e-01 1.13e+01 angle pdb=" N ARG A 456 " pdb=" CA ARG A 456 " pdb=" C ARG A 456 " ideal model delta sigma weight residual 109.31 113.91 -4.60 1.42e+00 4.96e-01 1.05e+01 angle pdb=" C ILE D 159 " pdb=" CA ILE D 159 " pdb=" CB ILE D 159 " ideal model delta sigma weight residual 113.70 110.76 2.94 9.50e-01 1.11e+00 9.59e+00 ... (remaining 19506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 8438 15.99 - 31.99: 211 31.99 - 47.98: 48 47.98 - 63.97: 13 63.97 - 79.97: 2 Dihedral angle restraints: 8712 sinusoidal: 3445 harmonic: 5267 Sorted by residual: dihedral pdb=" C ASN B 374 " pdb=" N ASN B 374 " pdb=" CA ASN B 374 " pdb=" CB ASN B 374 " ideal model delta harmonic sigma weight residual -122.60 -131.42 8.82 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA ARG A 334 " pdb=" CB ARG A 334 " pdb=" CG ARG A 334 " pdb=" CD ARG A 334 " ideal model delta sinusoidal sigma weight residual -60.00 -117.69 57.69 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG C 334 " pdb=" CB ARG C 334 " pdb=" CG ARG C 334 " pdb=" CD ARG C 334 " ideal model delta sinusoidal sigma weight residual -180.00 -122.96 -57.04 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1915 0.065 - 0.130: 300 0.130 - 0.195: 1 0.195 - 0.260: 1 0.260 - 0.325: 2 Chirality restraints: 2219 Sorted by residual: chirality pdb=" CA ASN B 374 " pdb=" N ASN B 374 " pdb=" C ASN B 374 " pdb=" CB ASN B 374 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA SER A 455 " pdb=" N SER A 455 " pdb=" C SER A 455 " pdb=" CB SER A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 375 " pdb=" CA VAL B 375 " pdb=" CG1 VAL B 375 " pdb=" CG2 VAL B 375 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2216 not shown) Planarity restraints: 2541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 266 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C LYS A 266 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS A 266 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 376 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO B 377 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 377 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 377 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 373 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.51e+00 pdb=" C SER B 373 " 0.027 2.00e-02 2.50e+03 pdb=" O SER B 373 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN B 374 " -0.009 2.00e-02 2.50e+03 ... (remaining 2538 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 132 2.57 - 3.15: 12595 3.15 - 3.74: 22654 3.74 - 4.32: 31219 4.32 - 4.90: 52197 Nonbonded interactions: 118797 Sorted by model distance: nonbonded pdb=" OG1 THR B 98 " pdb=" O ALA B 321 " model vdw 1.991 3.040 nonbonded pdb=" O LEU A 193 " pdb=" OG SER A 196 " model vdw 2.062 3.040 nonbonded pdb=" O LEU D 193 " pdb=" OG SER D 196 " model vdw 2.096 3.040 nonbonded pdb=" OG1 THR A 415 " pdb=" OH TYR A 428 " model vdw 2.141 3.040 nonbonded pdb=" OG SER A 348 " pdb=" OD1 ASN A 374 " model vdw 2.148 3.040 ... (remaining 118792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ h 476)) selection = chain 'B' selection = (chain 'C' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ h 476)) selection = (chain 'D' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ h 476)) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.750 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14398 Z= 0.122 Angle : 0.485 11.714 19511 Z= 0.275 Chirality : 0.042 0.325 2219 Planarity : 0.003 0.042 2541 Dihedral : 8.208 79.968 5328 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.20 % Allowed : 3.22 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1839 helix: 0.97 (0.17), residues: 807 sheet: -0.99 (0.26), residues: 318 loop : -1.92 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 484 HIS 0.002 0.000 HIS C 244 PHE 0.020 0.001 PHE A 459 TYR 0.007 0.001 TYR A 236 ARG 0.002 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.16689 ( 704) hydrogen bonds : angle 6.35882 ( 2049) covalent geometry : bond 0.00208 (14398) covalent geometry : angle 0.48487 (19511) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.7831 (mtm) cc_final: 0.7471 (mtm) REVERT: C 67 LEU cc_start: 0.8007 (mt) cc_final: 0.7260 (mp) REVERT: C 158 MET cc_start: 0.5848 (ttp) cc_final: 0.5336 (tmm) REVERT: C 168 MET cc_start: 0.7622 (mmt) cc_final: 0.7329 (mmt) REVERT: D 468 LYS cc_start: 0.2109 (mptt) cc_final: 0.1196 (mttt) outliers start: 3 outliers final: 2 residues processed: 412 average time/residue: 0.3118 time to fit residues: 177.7264 Evaluate side-chains 229 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 231 ASN A 318 GLN A 374 ASN A 404 GLN A 472 GLN B 78 GLN B 115 HIS B 194 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 283 GLN B 318 GLN B 476 GLN C 41 GLN C 78 GLN C 95 GLN C 207 HIS C 310 ASN C 318 GLN C 365 ASN C 430 HIS C 436 GLN C 472 GLN D 33 ASN D 95 GLN D 256 ASN D 318 GLN D 413 ASN D 472 GLN D 483 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.077032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059146 restraints weight = 64620.657| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.32 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.199 14398 Z= 0.334 Angle : 0.814 10.849 19511 Z= 0.417 Chirality : 0.049 0.203 2219 Planarity : 0.006 0.054 2541 Dihedral : 4.896 44.049 1948 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 3.49 % Allowed : 12.04 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1839 helix: 1.02 (0.17), residues: 824 sheet: -0.46 (0.27), residues: 318 loop : -1.43 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 162 HIS 0.012 0.002 HIS C 219 PHE 0.018 0.002 PHE C 418 TYR 0.023 0.003 TYR B 76 ARG 0.008 0.001 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 704) hydrogen bonds : angle 5.64755 ( 2049) covalent geometry : bond 0.00743 (14398) covalent geometry : angle 0.81362 (19511) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8978 (mt) cc_final: 0.8646 (tp) REVERT: A 176 MET cc_start: 0.8986 (tpt) cc_final: 0.8763 (tpp) REVERT: A 312 ARG cc_start: 0.9411 (mmp80) cc_final: 0.9196 (mtm-85) REVERT: A 379 MET cc_start: 0.7886 (mpt) cc_final: 0.7666 (mpt) REVERT: A 449 MET cc_start: 0.8712 (tmm) cc_final: 0.8056 (ptm) REVERT: A 472 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: B 158 MET cc_start: 0.6862 (tpt) cc_final: 0.6331 (tpp) REVERT: B 317 ASP cc_start: 0.9323 (p0) cc_final: 0.9001 (p0) REVERT: B 318 GLN cc_start: 0.9704 (mm-40) cc_final: 0.9409 (mm110) REVERT: B 361 TYR cc_start: 0.9229 (m-80) cc_final: 0.8918 (m-80) REVERT: B 468 LYS cc_start: 0.2157 (mttp) cc_final: 0.1794 (mttt) REVERT: C 71 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8810 (mp10) REVERT: C 128 MET cc_start: 0.8566 (ttm) cc_final: 0.8085 (tmm) REVERT: C 158 MET cc_start: 0.7865 (ttp) cc_final: 0.7320 (tmm) REVERT: C 162 TRP cc_start: 0.8492 (m-10) cc_final: 0.8126 (m-10) REVERT: C 387 PHE cc_start: 0.8653 (m-80) cc_final: 0.8227 (m-80) REVERT: C 468 LYS cc_start: 0.9345 (tptm) cc_final: 0.9107 (tptp) REVERT: D 90 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9391 (tp) REVERT: D 158 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7380 (ttp) REVERT: D 166 MET cc_start: 0.9029 (tpt) cc_final: 0.8786 (mmm) REVERT: D 379 MET cc_start: 0.8355 (mtp) cc_final: 0.8139 (mtp) REVERT: D 468 LYS cc_start: 0.2336 (mptt) cc_final: 0.1840 (mttp) outliers start: 53 outliers final: 33 residues processed: 238 average time/residue: 0.2962 time to fit residues: 105.2544 Evaluate side-chains 199 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 300 TRP Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 123 optimal weight: 0.0980 chunk 142 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 44 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN B 115 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.078977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.060984 restraints weight = 62789.218| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 5.40 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 14398 Z= 0.155 Angle : 0.665 12.915 19511 Z= 0.329 Chirality : 0.046 0.276 2219 Planarity : 0.004 0.039 2541 Dihedral : 4.680 50.669 1948 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.89 % Allowed : 12.89 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1839 helix: 1.40 (0.18), residues: 824 sheet: -0.32 (0.27), residues: 333 loop : -1.15 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 300 HIS 0.008 0.001 HIS B 115 PHE 0.023 0.001 PHE A 164 TYR 0.031 0.002 TYR B 411 ARG 0.005 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 704) hydrogen bonds : angle 5.13402 ( 2049) covalent geometry : bond 0.00369 (14398) covalent geometry : angle 0.66499 (19511) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8955 (mt) cc_final: 0.8663 (tp) REVERT: A 176 MET cc_start: 0.9075 (tpt) cc_final: 0.8767 (tpp) REVERT: A 379 MET cc_start: 0.7914 (mpt) cc_final: 0.7593 (mpt) REVERT: B 47 MET cc_start: 0.8729 (mtm) cc_final: 0.8288 (mtm) REVERT: B 158 MET cc_start: 0.7093 (tpt) cc_final: 0.6633 (tpp) REVERT: B 166 MET cc_start: 0.9237 (mmm) cc_final: 0.8941 (tpt) REVERT: B 181 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7866 (ptp-170) REVERT: B 255 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7838 (mmtt) REVERT: B 293 LEU cc_start: 0.9332 (mt) cc_final: 0.8696 (pp) REVERT: B 317 ASP cc_start: 0.9297 (p0) cc_final: 0.8912 (p0) REVERT: B 318 GLN cc_start: 0.9728 (mm-40) cc_final: 0.9393 (mm-40) REVERT: B 361 TYR cc_start: 0.9152 (m-80) cc_final: 0.8856 (m-80) REVERT: B 468 LYS cc_start: 0.1944 (mttp) cc_final: 0.1527 (mttt) REVERT: C 71 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8698 (mp10) REVERT: C 128 MET cc_start: 0.8502 (ttm) cc_final: 0.8014 (tmm) REVERT: C 158 MET cc_start: 0.7821 (ttp) cc_final: 0.7116 (tmm) REVERT: C 162 TRP cc_start: 0.8426 (m-10) cc_final: 0.7902 (m-10) REVERT: C 166 MET cc_start: 0.8800 (mmm) cc_final: 0.8499 (mmm) REVERT: C 182 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8735 (p) REVERT: C 387 PHE cc_start: 0.8491 (m-80) cc_final: 0.8105 (m-80) REVERT: D 124 MET cc_start: 0.8752 (tpt) cc_final: 0.8417 (tpt) REVERT: D 158 MET cc_start: 0.7512 (ttm) cc_final: 0.7203 (tpp) REVERT: D 261 MET cc_start: 0.7190 (mmt) cc_final: 0.6918 (mmt) outliers start: 44 outliers final: 27 residues processed: 226 average time/residue: 0.4054 time to fit residues: 134.4908 Evaluate side-chains 203 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 181 ARG Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 173 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 115 HIS B 430 HIS C 41 GLN C 209 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 77 GLN D 244 HIS ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.076610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.058654 restraints weight = 63873.868| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 5.27 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 14398 Z= 0.259 Angle : 0.714 11.996 19511 Z= 0.362 Chirality : 0.046 0.206 2219 Planarity : 0.005 0.039 2541 Dihedral : 5.055 58.689 1948 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.08 % Allowed : 12.70 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1839 helix: 1.33 (0.18), residues: 823 sheet: -0.29 (0.28), residues: 329 loop : -1.13 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 162 HIS 0.014 0.002 HIS B 115 PHE 0.016 0.002 PHE A 164 TYR 0.010 0.002 TYR C 428 ARG 0.004 0.001 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 704) hydrogen bonds : angle 5.40261 ( 2049) covalent geometry : bond 0.00594 (14398) covalent geometry : angle 0.71355 (19511) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.9071 (tpt) cc_final: 0.8741 (tpp) REVERT: A 286 MET cc_start: 0.7808 (pmm) cc_final: 0.7523 (pmm) REVERT: B 20 LYS cc_start: 0.9237 (pttm) cc_final: 0.8999 (mmmt) REVERT: B 158 MET cc_start: 0.7329 (tpt) cc_final: 0.6701 (tpp) REVERT: B 168 MET cc_start: 0.8669 (mmm) cc_final: 0.8439 (mmm) REVERT: B 255 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8034 (mmtt) REVERT: B 317 ASP cc_start: 0.9338 (p0) cc_final: 0.9031 (p0) REVERT: B 318 GLN cc_start: 0.9748 (mm-40) cc_final: 0.9431 (mm110) REVERT: B 361 TYR cc_start: 0.9215 (m-80) cc_final: 0.8988 (m-80) REVERT: B 468 LYS cc_start: 0.1778 (mttp) cc_final: 0.1453 (mttt) REVERT: C 158 MET cc_start: 0.7860 (ttp) cc_final: 0.7327 (tmm) REVERT: C 162 TRP cc_start: 0.8505 (m-10) cc_final: 0.8000 (m-10) REVERT: C 166 MET cc_start: 0.8924 (mmm) cc_final: 0.8597 (mmm) REVERT: C 182 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8712 (p) REVERT: C 387 PHE cc_start: 0.8542 (m-80) cc_final: 0.8125 (m-80) REVERT: D 90 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9350 (tp) REVERT: D 166 MET cc_start: 0.9019 (tpt) cc_final: 0.8709 (mmm) outliers start: 62 outliers final: 42 residues processed: 220 average time/residue: 0.2575 time to fit residues: 84.2410 Evaluate side-chains 208 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS C 41 GLN D 33 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.076820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.059026 restraints weight = 63699.298| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.27 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 14398 Z= 0.193 Angle : 0.688 12.662 19511 Z= 0.341 Chirality : 0.046 0.305 2219 Planarity : 0.004 0.038 2541 Dihedral : 4.811 49.118 1946 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.14 % Allowed : 14.14 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1839 helix: 1.45 (0.18), residues: 823 sheet: -0.28 (0.28), residues: 329 loop : -0.98 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 162 HIS 0.010 0.001 HIS B 115 PHE 0.015 0.002 PHE D 215 TYR 0.009 0.001 TYR A 382 ARG 0.007 0.001 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 704) hydrogen bonds : angle 5.27001 ( 2049) covalent geometry : bond 0.00448 (14398) covalent geometry : angle 0.68807 (19511) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9222 (ptpp) cc_final: 0.8978 (ptpp) REVERT: A 73 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8759 (tp) REVERT: A 87 ILE cc_start: 0.8910 (mt) cc_final: 0.8688 (tp) REVERT: A 176 MET cc_start: 0.9084 (tpt) cc_final: 0.8731 (tpp) REVERT: A 286 MET cc_start: 0.7815 (pmm) cc_final: 0.7541 (pmm) REVERT: B 20 LYS cc_start: 0.9258 (pttm) cc_final: 0.9025 (mmmt) REVERT: B 158 MET cc_start: 0.8050 (tpt) cc_final: 0.7485 (tpp) REVERT: B 317 ASP cc_start: 0.9311 (p0) cc_final: 0.9032 (p0) REVERT: B 318 GLN cc_start: 0.9743 (mm-40) cc_final: 0.9434 (mp10) REVERT: B 361 TYR cc_start: 0.9200 (m-80) cc_final: 0.8936 (m-80) REVERT: B 468 LYS cc_start: 0.1738 (mttp) cc_final: 0.1330 (mttt) REVERT: C 71 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8764 (mp10) REVERT: C 128 MET cc_start: 0.8367 (ttp) cc_final: 0.7946 (tmm) REVERT: C 158 MET cc_start: 0.7830 (ttp) cc_final: 0.7258 (tmm) REVERT: C 162 TRP cc_start: 0.8533 (m-10) cc_final: 0.7977 (m-10) REVERT: C 166 MET cc_start: 0.8823 (mmm) cc_final: 0.8472 (mmm) REVERT: C 387 PHE cc_start: 0.8456 (m-80) cc_final: 0.8055 (m-80) REVERT: D 90 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9346 (tp) REVERT: D 166 MET cc_start: 0.8982 (tpt) cc_final: 0.8714 (mmm) outliers start: 63 outliers final: 41 residues processed: 230 average time/residue: 0.2396 time to fit residues: 82.2536 Evaluate side-chains 212 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS C 41 GLN D 307 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.077820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.060051 restraints weight = 63708.301| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 5.32 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14398 Z= 0.138 Angle : 0.663 13.508 19511 Z= 0.327 Chirality : 0.046 0.234 2219 Planarity : 0.004 0.039 2541 Dihedral : 4.691 50.170 1946 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.55 % Allowed : 15.33 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1839 helix: 1.56 (0.18), residues: 823 sheet: -0.25 (0.28), residues: 332 loop : -0.91 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 162 HIS 0.007 0.001 HIS B 430 PHE 0.025 0.001 PHE A 164 TYR 0.024 0.001 TYR A 382 ARG 0.006 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 704) hydrogen bonds : angle 5.10573 ( 2049) covalent geometry : bond 0.00329 (14398) covalent geometry : angle 0.66345 (19511) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9232 (ptpp) cc_final: 0.9000 (ptpp) REVERT: A 87 ILE cc_start: 0.8890 (mt) cc_final: 0.8682 (tp) REVERT: A 163 MET cc_start: 0.8461 (mtm) cc_final: 0.8083 (ptt) REVERT: A 286 MET cc_start: 0.7786 (pmm) cc_final: 0.7468 (pmm) REVERT: B 20 LYS cc_start: 0.9328 (pttm) cc_final: 0.9112 (mmmt) REVERT: B 77 GLN cc_start: 0.9485 (OUTLIER) cc_final: 0.9233 (tm-30) REVERT: B 158 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7183 (tpp) REVERT: B 168 MET cc_start: 0.8746 (mmm) cc_final: 0.8441 (mmm) REVERT: B 317 ASP cc_start: 0.9277 (p0) cc_final: 0.8921 (p0) REVERT: B 318 GLN cc_start: 0.9733 (mm-40) cc_final: 0.9408 (mm-40) REVERT: B 361 TYR cc_start: 0.9155 (m-80) cc_final: 0.8891 (m-80) REVERT: B 428 TYR cc_start: 0.9069 (t80) cc_final: 0.8710 (t80) REVERT: B 468 LYS cc_start: 0.1917 (mttp) cc_final: 0.1523 (mttm) REVERT: C 41 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: C 71 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8736 (mp10) REVERT: C 128 MET cc_start: 0.8349 (ttp) cc_final: 0.7934 (tmm) REVERT: C 158 MET cc_start: 0.7826 (ttp) cc_final: 0.7183 (tmm) REVERT: C 162 TRP cc_start: 0.8470 (m-10) cc_final: 0.7835 (m-10) REVERT: C 166 MET cc_start: 0.8813 (mmm) cc_final: 0.8423 (mmm) REVERT: C 387 PHE cc_start: 0.8423 (m-80) cc_final: 0.7998 (m-80) REVERT: D 90 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9356 (tp) REVERT: D 166 MET cc_start: 0.8962 (tpt) cc_final: 0.8739 (mmm) REVERT: D 247 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.7782 (mmt180) REVERT: D 252 MET cc_start: 0.7123 (pmm) cc_final: 0.6843 (pmm) outliers start: 54 outliers final: 37 residues processed: 228 average time/residue: 0.2574 time to fit residues: 86.7184 Evaluate side-chains 214 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS C 41 GLN C 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.077144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.059392 restraints weight = 64553.360| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 5.33 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 14398 Z= 0.175 Angle : 0.690 14.061 19511 Z= 0.342 Chirality : 0.046 0.192 2219 Planarity : 0.004 0.049 2541 Dihedral : 4.728 50.487 1946 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.95 % Allowed : 15.79 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1839 helix: 1.49 (0.18), residues: 824 sheet: -0.24 (0.28), residues: 331 loop : -0.90 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 162 HIS 0.006 0.001 HIS C 219 PHE 0.014 0.001 PHE C 164 TYR 0.010 0.001 TYR A 138 ARG 0.009 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 704) hydrogen bonds : angle 5.16733 ( 2049) covalent geometry : bond 0.00414 (14398) covalent geometry : angle 0.68990 (19511) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9238 (ptpp) cc_final: 0.8977 (ptpp) REVERT: A 73 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 87 ILE cc_start: 0.8902 (mt) cc_final: 0.8689 (tp) REVERT: A 252 MET cc_start: 0.8112 (mtt) cc_final: 0.7862 (mmm) REVERT: A 286 MET cc_start: 0.7761 (pmm) cc_final: 0.7507 (pmm) REVERT: B 20 LYS cc_start: 0.9293 (pttm) cc_final: 0.9073 (mmmt) REVERT: B 75 ARG cc_start: 0.9186 (tpm170) cc_final: 0.8864 (tpm170) REVERT: B 168 MET cc_start: 0.8803 (mmm) cc_final: 0.8505 (mmm) REVERT: B 267 GLU cc_start: 0.9000 (mp0) cc_final: 0.8619 (pm20) REVERT: B 293 LEU cc_start: 0.9421 (mt) cc_final: 0.9136 (tp) REVERT: B 317 ASP cc_start: 0.9325 (p0) cc_final: 0.9059 (p0) REVERT: B 318 GLN cc_start: 0.9741 (mm-40) cc_final: 0.9433 (mp10) REVERT: B 361 TYR cc_start: 0.9165 (m-80) cc_final: 0.8898 (m-80) REVERT: B 428 TYR cc_start: 0.9082 (t80) cc_final: 0.8859 (t80) REVERT: B 468 LYS cc_start: 0.1828 (mttp) cc_final: 0.1479 (mttt) REVERT: C 71 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8671 (mp10) REVERT: C 128 MET cc_start: 0.8341 (ttp) cc_final: 0.7922 (tmm) REVERT: C 132 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7399 (p) REVERT: C 158 MET cc_start: 0.7819 (ttp) cc_final: 0.7014 (tmm) REVERT: C 162 TRP cc_start: 0.8517 (m-10) cc_final: 0.7855 (m-10) REVERT: C 166 MET cc_start: 0.8828 (mmm) cc_final: 0.8479 (mmm) REVERT: C 387 PHE cc_start: 0.8414 (m-80) cc_final: 0.8005 (m-80) REVERT: C 449 MET cc_start: 0.6181 (tmm) cc_final: 0.5872 (tmm) REVERT: D 90 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9369 (tp) REVERT: D 158 MET cc_start: 0.7296 (tpp) cc_final: 0.7024 (tpp) REVERT: D 252 MET cc_start: 0.7172 (pmm) cc_final: 0.6877 (pmm) outliers start: 60 outliers final: 43 residues processed: 218 average time/residue: 0.2638 time to fit residues: 86.0655 Evaluate side-chains 216 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.077251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.059590 restraints weight = 63635.669| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 5.28 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 14398 Z= 0.158 Angle : 0.684 15.008 19511 Z= 0.337 Chirality : 0.046 0.338 2219 Planarity : 0.004 0.053 2541 Dihedral : 4.717 51.443 1946 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.62 % Allowed : 15.99 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1839 helix: 1.51 (0.18), residues: 826 sheet: -0.36 (0.28), residues: 345 loop : -0.84 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 162 HIS 0.006 0.001 HIS C 219 PHE 0.022 0.001 PHE A 164 TYR 0.037 0.002 TYR B 76 ARG 0.008 0.000 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 704) hydrogen bonds : angle 5.11102 ( 2049) covalent geometry : bond 0.00379 (14398) covalent geometry : angle 0.68448 (19511) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8990 (ptpp) REVERT: A 73 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8688 (tp) REVERT: A 286 MET cc_start: 0.7634 (pmm) cc_final: 0.7342 (pmm) REVERT: B 20 LYS cc_start: 0.9332 (pttm) cc_final: 0.9117 (mmmt) REVERT: B 75 ARG cc_start: 0.9198 (tpm170) cc_final: 0.8858 (tpm170) REVERT: B 158 MET cc_start: 0.7583 (tpp) cc_final: 0.7246 (tpp) REVERT: B 267 GLU cc_start: 0.8969 (mp0) cc_final: 0.8607 (pm20) REVERT: B 293 LEU cc_start: 0.9389 (mt) cc_final: 0.9118 (tp) REVERT: B 318 GLN cc_start: 0.9745 (mm-40) cc_final: 0.9510 (mm110) REVERT: B 361 TYR cc_start: 0.9169 (m-80) cc_final: 0.8949 (m-80) REVERT: B 428 TYR cc_start: 0.9075 (t80) cc_final: 0.8847 (t80) REVERT: B 468 LYS cc_start: 0.1806 (mttp) cc_final: 0.1472 (mttt) REVERT: C 71 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8665 (mp10) REVERT: C 128 MET cc_start: 0.8358 (ttp) cc_final: 0.7935 (tmm) REVERT: C 132 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7400 (p) REVERT: C 166 MET cc_start: 0.8826 (mmm) cc_final: 0.8470 (mmm) REVERT: C 387 PHE cc_start: 0.8382 (m-80) cc_final: 0.7980 (m-80) REVERT: D 90 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9382 (tp) REVERT: D 158 MET cc_start: 0.7312 (tpp) cc_final: 0.7052 (tpp) REVERT: D 247 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.7823 (mmt180) REVERT: D 252 MET cc_start: 0.7149 (pmm) cc_final: 0.6820 (pmm) outliers start: 55 outliers final: 43 residues processed: 212 average time/residue: 0.2501 time to fit residues: 78.6960 Evaluate side-chains 218 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 50.0000 chunk 132 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.075585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.057810 restraints weight = 64505.621| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 5.27 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 14398 Z= 0.249 Angle : 0.761 15.500 19511 Z= 0.380 Chirality : 0.047 0.303 2219 Planarity : 0.005 0.050 2541 Dihedral : 4.851 24.866 1944 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.42 % Allowed : 16.25 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1839 helix: 1.39 (0.18), residues: 826 sheet: -0.31 (0.28), residues: 332 loop : -0.94 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A 162 HIS 0.018 0.002 HIS B 115 PHE 0.016 0.002 PHE A 227 TYR 0.019 0.002 TYR D 428 ARG 0.019 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 704) hydrogen bonds : angle 5.40301 ( 2049) covalent geometry : bond 0.00579 (14398) covalent geometry : angle 0.76111 (19511) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9015 (ptpp) REVERT: A 55 LYS cc_start: 0.9602 (tttt) cc_final: 0.9337 (tttt) REVERT: A 252 MET cc_start: 0.8015 (mmm) cc_final: 0.7810 (mmm) REVERT: A 286 MET cc_start: 0.7628 (pmm) cc_final: 0.7367 (pmm) REVERT: B 20 LYS cc_start: 0.9339 (pttm) cc_final: 0.9119 (mmmt) REVERT: B 75 ARG cc_start: 0.9213 (tpm170) cc_final: 0.8889 (tpm170) REVERT: B 158 MET cc_start: 0.7765 (tpp) cc_final: 0.7503 (tpp) REVERT: B 168 MET cc_start: 0.8826 (mmm) cc_final: 0.8577 (mmm) REVERT: B 267 GLU cc_start: 0.8992 (mp0) cc_final: 0.8606 (pm20) REVERT: B 293 LEU cc_start: 0.9437 (mt) cc_final: 0.9148 (tp) REVERT: B 468 LYS cc_start: 0.1669 (mttp) cc_final: 0.1373 (mttt) REVERT: C 71 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: C 128 MET cc_start: 0.8373 (ttp) cc_final: 0.7996 (tmm) REVERT: C 163 MET cc_start: 0.8398 (mtm) cc_final: 0.8156 (mtm) REVERT: C 166 MET cc_start: 0.8888 (mmm) cc_final: 0.8541 (mmm) REVERT: C 387 PHE cc_start: 0.8486 (m-80) cc_final: 0.8037 (m-80) REVERT: D 90 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9396 (tp) REVERT: D 158 MET cc_start: 0.7481 (tpp) cc_final: 0.7217 (tpp) REVERT: D 166 MET cc_start: 0.9018 (tpt) cc_final: 0.8725 (tpt) REVERT: D 261 MET cc_start: 0.7214 (mmt) cc_final: 0.6747 (mmm) REVERT: D 474 TYR cc_start: 0.9039 (m-80) cc_final: 0.8730 (m-80) outliers start: 52 outliers final: 41 residues processed: 205 average time/residue: 0.2795 time to fit residues: 86.2273 Evaluate side-chains 205 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 152 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 72 optimal weight: 0.0980 chunk 136 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 265 ASN B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 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 = 0.3914 r_free = 0.3914 target = 0.076572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.058835 restraints weight = 64188.671| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.30 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 14398 Z= 0.180 Angle : 0.743 16.838 19511 Z= 0.367 Chirality : 0.047 0.333 2219 Planarity : 0.005 0.067 2541 Dihedral : 4.799 30.666 1944 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.09 % Allowed : 16.84 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1839 helix: 1.45 (0.18), residues: 825 sheet: -0.33 (0.28), residues: 330 loop : -0.92 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 162 HIS 0.007 0.001 HIS C 219 PHE 0.024 0.002 PHE A 164 TYR 0.030 0.002 TYR A 382 ARG 0.017 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 704) hydrogen bonds : angle 5.25709 ( 2049) covalent geometry : bond 0.00428 (14398) covalent geometry : angle 0.74316 (19511) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9292 (ptpp) cc_final: 0.9050 (ptpp) REVERT: A 55 LYS cc_start: 0.9605 (tttt) cc_final: 0.9231 (mttt) REVERT: B 20 LYS cc_start: 0.9344 (pttm) cc_final: 0.9126 (mmmt) REVERT: B 75 ARG cc_start: 0.9174 (tpm170) cc_final: 0.8822 (tpm170) REVERT: B 158 MET cc_start: 0.7624 (tpp) cc_final: 0.7246 (tpp) REVERT: B 168 MET cc_start: 0.8843 (mmm) cc_final: 0.8579 (mmm) REVERT: B 255 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7536 (mmtt) REVERT: B 309 LYS cc_start: 0.9251 (ptpp) cc_final: 0.9006 (ptpp) REVERT: B 317 ASP cc_start: 0.9330 (p0) cc_final: 0.9082 (p0) REVERT: B 318 GLN cc_start: 0.9780 (mm-40) cc_final: 0.9405 (mp10) REVERT: B 428 TYR cc_start: 0.9100 (t80) cc_final: 0.8876 (t80) REVERT: B 468 LYS cc_start: 0.1618 (mttp) cc_final: 0.1300 (mttt) REVERT: C 71 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8726 (mp10) REVERT: C 128 MET cc_start: 0.8391 (ttp) cc_final: 0.8015 (tmm) REVERT: C 166 MET cc_start: 0.8842 (mmm) cc_final: 0.8481 (mmm) REVERT: C 387 PHE cc_start: 0.8434 (m-80) cc_final: 0.7989 (m-80) REVERT: D 90 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9377 (tp) REVERT: D 158 MET cc_start: 0.7503 (tpp) cc_final: 0.7244 (tpp) REVERT: D 166 MET cc_start: 0.9017 (tpt) cc_final: 0.8756 (tpt) REVERT: D 261 MET cc_start: 0.7011 (mmt) cc_final: 0.6533 (mmm) REVERT: D 474 TYR cc_start: 0.9033 (m-80) cc_final: 0.8676 (m-80) outliers start: 47 outliers final: 41 residues processed: 202 average time/residue: 0.3813 time to fit residues: 120.9897 Evaluate side-chains 207 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 80 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.077718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.059848 restraints weight = 63903.713| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 5.46 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14398 Z= 0.140 Angle : 0.729 17.535 19511 Z= 0.356 Chirality : 0.046 0.315 2219 Planarity : 0.004 0.060 2541 Dihedral : 4.652 31.184 1944 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.83 % Allowed : 17.17 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1839 helix: 1.48 (0.18), residues: 825 sheet: -0.36 (0.28), residues: 334 loop : -0.86 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP A 162 HIS 0.005 0.001 HIS C 219 PHE 0.020 0.001 PHE C 155 TYR 0.030 0.002 TYR A 382 ARG 0.017 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 704) hydrogen bonds : angle 5.09717 ( 2049) covalent geometry : bond 0.00338 (14398) covalent geometry : angle 0.72869 (19511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7835.51 seconds wall clock time: 141 minutes 2.78 seconds (8462.78 seconds total)