Starting phenix.real_space_refine on Sat Aug 23 18:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izv_61043/08_2025/9izv_61043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izv_61043/08_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_61043/08_2025/9izv_61043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izv_61043/08_2025/9izv_61043.map" model { file = "/net/cci-nas-00/data/ceres_data/9izv_61043/08_2025/9izv_61043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izv_61043/08_2025/9izv_61043.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.044 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.05, per 1000 atoms: 0.22 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: 1.22 Conformation dependent library (CDL) restraints added in 687.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.33 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: 1.78 Time building geometry restraints manager: 1.68 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: 1.510 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 12.580 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG B 181 TYR 0.007 0.001 TYR A 236 PHE 0.020 0.001 PHE A 459 TRP 0.004 0.000 TRP C 484 HIS 0.002 0.000 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00208 (14398) covalent geometry : angle 0.48487 (19511) hydrogen bonds : bond 0.16689 ( 704) hydrogen bonds : angle 6.35882 ( 2049) *********************** 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 : 0.471 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: 0.7330 (mmt) REVERT: D 468 LYS cc_start: 0.2109 (mptt) cc_final: 0.1195 (mttt) outliers start: 3 outliers final: 2 residues processed: 412 average time/residue: 0.1156 time to fit residues: 66.8590 Evaluate side-chains 225 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 207 HIS A 231 ASN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 374 ASN B 41 GLN B 78 GLN B 115 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 231 ASN B 272 GLN B 476 GLN C 78 GLN C 95 GLN C 207 HIS C 244 HIS C 318 GLN C 365 ASN C 430 HIS C 436 GLN C 472 GLN D 204 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 436 GLN D 472 GLN D 483 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.083222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.065635 restraints weight = 61435.909| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 5.47 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14398 Z= 0.152 Angle : 0.688 12.900 19511 Z= 0.341 Chirality : 0.046 0.180 2219 Planarity : 0.005 0.050 2541 Dihedral : 3.990 43.916 1948 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 12.50 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1839 helix: 1.46 (0.18), residues: 820 sheet: -0.44 (0.27), residues: 321 loop : -1.27 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 108 TYR 0.028 0.002 TYR B 411 PHE 0.019 0.001 PHE A 164 TRP 0.025 0.002 TRP D 162 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00354 (14398) covalent geometry : angle 0.68830 (19511) hydrogen bonds : bond 0.03893 ( 704) hydrogen bonds : angle 5.14450 ( 2049) *********************** 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 275 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.417 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 73 LEU cc_start: 0.9256 (mm) cc_final: 0.8987 (tp) REVERT: A 114 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8787 (mm-30) REVERT: A 176 MET cc_start: 0.8935 (tpt) cc_final: 0.8256 (tpt) REVERT: A 252 MET cc_start: 0.7819 (mtt) cc_final: 0.7388 (ttm) REVERT: A 379 MET cc_start: 0.7892 (mpt) cc_final: 0.7628 (mpt) REVERT: A 449 MET cc_start: 0.8663 (tmm) cc_final: 0.7892 (ptm) REVERT: B 47 MET cc_start: 0.8804 (mtm) cc_final: 0.8481 (mtm) REVERT: B 95 GLN cc_start: 0.6695 (tt0) cc_final: 0.6220 (tm-30) REVERT: B 158 MET cc_start: 0.6591 (tpt) cc_final: 0.6007 (tpp) REVERT: B 166 MET cc_start: 0.9400 (mmt) cc_final: 0.9154 (mmm) REVERT: B 268 ASN cc_start: 0.8901 (m-40) cc_final: 0.8510 (m110) REVERT: B 361 TYR cc_start: 0.9120 (m-80) cc_final: 0.8476 (m-80) REVERT: B 428 TYR cc_start: 0.8860 (t80) cc_final: 0.8596 (t80) REVERT: C 67 LEU cc_start: 0.9217 (mt) cc_final: 0.8643 (mt) REVERT: C 71 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: C 158 MET cc_start: 0.7607 (ttp) cc_final: 0.7247 (tmm) REVERT: C 162 TRP cc_start: 0.8255 (m-10) cc_final: 0.7748 (m-10) REVERT: C 166 MET cc_start: 0.8876 (mmm) cc_final: 0.8659 (mmm) REVERT: C 261 MET cc_start: 0.8187 (mmt) cc_final: 0.7910 (mmt) REVERT: C 300 TRP cc_start: 0.7542 (OUTLIER) cc_final: 0.7081 (m-90) REVERT: C 317 ASP cc_start: 0.8024 (p0) cc_final: 0.7620 (p0) REVERT: C 318 GLN cc_start: 0.9137 (mt0) cc_final: 0.8756 (mp10) REVERT: C 361 TYR cc_start: 0.9054 (m-80) cc_final: 0.8542 (m-80) REVERT: D 247 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.7939 (mmt180) REVERT: D 449 MET cc_start: 0.1309 (OUTLIER) cc_final: 0.1053 (ttt) REVERT: D 468 LYS cc_start: 0.2198 (mptt) cc_final: 0.1758 (mttt) outliers start: 33 outliers final: 17 residues processed: 268 average time/residue: 0.1040 time to fit residues: 40.8735 Evaluate side-chains 218 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR 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 207 HIS Chi-restraints excluded: chain B residue 259 VAL 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 B residue 447 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 449 MET 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 68 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 41 optimal weight: 40.0000 chunk 114 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 70 GLN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 115 HIS B 207 HIS B 283 GLN C 41 GLN D 33 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.080597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.062676 restraints weight = 62434.619| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 5.42 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 14398 Z= 0.172 Angle : 0.656 11.685 19511 Z= 0.326 Chirality : 0.045 0.263 2219 Planarity : 0.004 0.040 2541 Dihedral : 4.312 45.672 1948 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.09 % Allowed : 11.51 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.20), residues: 1839 helix: 1.54 (0.18), residues: 822 sheet: -0.35 (0.27), residues: 322 loop : -1.12 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 108 TYR 0.034 0.002 TYR D 76 PHE 0.020 0.001 PHE A 164 TRP 0.022 0.002 TRP D 162 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00407 (14398) covalent geometry : angle 0.65598 (19511) hydrogen bonds : bond 0.03564 ( 704) hydrogen bonds : angle 5.03114 ( 2049) *********************** 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 246 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.501 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: A 114 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8836 (mm-30) REVERT: A 158 MET cc_start: 0.8289 (mtm) cc_final: 0.7376 (ttp) REVERT: A 162 TRP cc_start: 0.8015 (m-10) cc_final: 0.7309 (m-10) REVERT: A 164 PHE cc_start: 0.9353 (p90) cc_final: 0.9138 (p90) REVERT: A 176 MET cc_start: 0.8972 (tpt) cc_final: 0.8509 (tpp) REVERT: A 252 MET cc_start: 0.8029 (mtt) cc_final: 0.7698 (mtt) REVERT: B 95 GLN cc_start: 0.6816 (tt0) cc_final: 0.6542 (tm-30) REVERT: B 158 MET cc_start: 0.6743 (tpt) cc_final: 0.6090 (tpp) REVERT: B 255 LYS cc_start: 0.8431 (mmtt) cc_final: 0.7931 (mmtt) REVERT: B 379 MET cc_start: 0.8065 (mpt) cc_final: 0.7779 (mmm) REVERT: B 428 TYR cc_start: 0.8977 (t80) cc_final: 0.8734 (t80) REVERT: B 468 LYS cc_start: 0.3935 (mttt) cc_final: 0.3707 (mttp) REVERT: C 67 LEU cc_start: 0.9287 (mt) cc_final: 0.8814 (mt) REVERT: C 71 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8749 (mp10) REVERT: C 128 MET cc_start: 0.8541 (ttm) cc_final: 0.8267 (tpp) REVERT: C 158 MET cc_start: 0.7604 (ttp) cc_final: 0.7149 (tmm) REVERT: C 162 TRP cc_start: 0.8372 (m-10) cc_final: 0.7738 (m-10) REVERT: C 166 MET cc_start: 0.8868 (mmm) cc_final: 0.8527 (mmm) REVERT: C 182 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 261 MET cc_start: 0.7992 (mmt) cc_final: 0.7736 (mmt) REVERT: D 158 MET cc_start: 0.7662 (ttm) cc_final: 0.7354 (tpp) REVERT: D 166 MET cc_start: 0.8869 (tpt) cc_final: 0.8473 (tpt) REVERT: D 247 ARG cc_start: 0.8672 (mtt-85) cc_final: 0.7894 (mmt180) REVERT: D 468 LYS cc_start: 0.2405 (mptt) cc_final: 0.1696 (mttp) outliers start: 47 outliers final: 32 residues processed: 237 average time/residue: 0.0996 time to fit residues: 35.4025 Evaluate side-chains 213 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR 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 93 LEU 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 375 VAL Chi-restraints excluded: chain B residue 392 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 112 VAL Chi-restraints excluded: chain C residue 132 THR 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 296 GLU 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 259 VAL 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 437 VAL 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 130 optimal weight: 0.7980 chunk 56 optimal weight: 0.0010 chunk 153 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 27 optimal weight: 50.0000 chunk 135 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 172 optimal weight: 0.0670 overall best weight: 0.7126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS B 115 HIS C 41 GLN D 33 ASN D 140 HIS D 307 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.082004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.064180 restraints weight = 61690.162| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 5.45 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14398 Z= 0.115 Angle : 0.628 10.078 19511 Z= 0.308 Chirality : 0.045 0.270 2219 Planarity : 0.004 0.041 2541 Dihedral : 4.260 47.740 1948 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.70 % Allowed : 12.96 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.20), residues: 1839 helix: 1.67 (0.19), residues: 823 sheet: -0.26 (0.27), residues: 331 loop : -0.98 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 108 TYR 0.012 0.001 TYR B 76 PHE 0.023 0.001 PHE A 164 TRP 0.035 0.002 TRP C 300 HIS 0.008 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00266 (14398) covalent geometry : angle 0.62828 (19511) hydrogen bonds : bond 0.03168 ( 704) hydrogen bonds : angle 4.83476 ( 2049) *********************** 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 245 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.501 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 114 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8801 (mm-30) REVERT: A 158 MET cc_start: 0.8196 (mtm) cc_final: 0.7299 (ttp) REVERT: A 162 TRP cc_start: 0.8028 (m-10) cc_final: 0.7287 (m-10) REVERT: A 176 MET cc_start: 0.8957 (tpt) cc_final: 0.8508 (tpp) REVERT: B 20 LYS cc_start: 0.9208 (pttm) cc_final: 0.8948 (mmmt) REVERT: B 71 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9300 (mp10) REVERT: B 95 GLN cc_start: 0.6932 (tt0) cc_final: 0.6546 (tm-30) REVERT: B 158 MET cc_start: 0.6778 (tpt) cc_final: 0.6299 (tpp) REVERT: B 168 MET cc_start: 0.8736 (mmm) cc_final: 0.8510 (mmm) REVERT: B 181 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7830 (ptp-170) REVERT: B 428 TYR cc_start: 0.9033 (t80) cc_final: 0.8743 (t80) REVERT: B 468 LYS cc_start: 0.3852 (mttt) cc_final: 0.3530 (mttp) REVERT: C 67 LEU cc_start: 0.9223 (mt) cc_final: 0.8693 (mt) REVERT: C 71 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8690 (mp10) REVERT: C 158 MET cc_start: 0.7464 (ttp) cc_final: 0.6781 (tmm) REVERT: C 162 TRP cc_start: 0.8283 (m-10) cc_final: 0.7627 (m-10) REVERT: C 166 MET cc_start: 0.8757 (mmm) cc_final: 0.8392 (mmm) REVERT: C 182 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8689 (p) REVERT: D 76 TYR cc_start: 0.9566 (t80) cc_final: 0.9346 (t80) REVERT: D 90 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9262 (tp) REVERT: D 158 MET cc_start: 0.7545 (ttm) cc_final: 0.7246 (tpp) REVERT: D 176 MET cc_start: 0.8164 (tpp) cc_final: 0.7905 (tpp) REVERT: D 247 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.7872 (mmt180) REVERT: D 428 TYR cc_start: 0.8768 (t80) cc_final: 0.8562 (t80) REVERT: D 468 LYS cc_start: 0.2349 (mptt) cc_final: 0.1896 (mttt) outliers start: 41 outliers final: 20 residues processed: 237 average time/residue: 0.0980 time to fit residues: 34.5906 Evaluate side-chains 218 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 71 GLN 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 181 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 132 THR 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 300 TRP Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 431 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 30 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 207 HIS B 251 ASN B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 140 HIS D 204 ASN D 244 HIS D 256 ASN D 413 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.076344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.058472 restraints weight = 64199.237| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 5.29 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4606 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= 0.300 Angle : 0.759 13.520 19511 Z= 0.385 Chirality : 0.047 0.208 2219 Planarity : 0.005 0.040 2541 Dihedral : 4.789 49.441 1946 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.82 % Allowed : 13.55 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.20), residues: 1839 helix: 1.45 (0.18), residues: 827 sheet: -0.36 (0.28), residues: 319 loop : -1.01 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 312 TYR 0.020 0.002 TYR B 76 PHE 0.026 0.002 PHE D 215 TRP 0.032 0.003 TRP C 300 HIS 0.026 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00676 (14398) covalent geometry : angle 0.75929 (19511) hydrogen bonds : bond 0.03980 ( 704) hydrogen bonds : angle 5.36553 ( 2049) *********************** 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 228 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.516 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 114 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8863 (mm-30) REVERT: A 158 MET cc_start: 0.8411 (mtm) cc_final: 0.7531 (ttt) REVERT: A 162 TRP cc_start: 0.8270 (m-10) cc_final: 0.7679 (m-10) REVERT: A 163 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8137 (ptt) REVERT: A 176 MET cc_start: 0.9010 (tpt) cc_final: 0.8572 (tpp) REVERT: B 20 LYS cc_start: 0.9229 (pttm) cc_final: 0.8956 (mmmt) REVERT: B 75 ARG cc_start: 0.9267 (tpm170) cc_final: 0.8896 (tpm170) REVERT: B 76 TYR cc_start: 0.9660 (t80) cc_final: 0.9327 (t80) REVERT: B 158 MET cc_start: 0.7183 (tpt) cc_final: 0.6597 (tpp) REVERT: B 255 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7680 (mmtt) REVERT: B 361 TYR cc_start: 0.9136 (m-80) cc_final: 0.8865 (m-80) REVERT: C 71 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: C 128 MET cc_start: 0.8605 (ttm) cc_final: 0.8036 (tmm) REVERT: C 158 MET cc_start: 0.7855 (ttp) cc_final: 0.7341 (tmm) REVERT: C 162 TRP cc_start: 0.8564 (m-10) cc_final: 0.7915 (m-10) REVERT: C 166 MET cc_start: 0.8900 (mmm) cc_final: 0.8487 (mmm) REVERT: C 387 PHE cc_start: 0.8532 (m-80) cc_final: 0.8171 (m-80) REVERT: D 90 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9418 (tp) REVERT: D 261 MET cc_start: 0.7396 (mmt) cc_final: 0.7187 (mmt) REVERT: D 428 TYR cc_start: 0.8830 (t80) cc_final: 0.8560 (t80) outliers start: 58 outliers final: 39 residues processed: 215 average time/residue: 0.1183 time to fit residues: 38.2492 Evaluate side-chains 199 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 452 PHE 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 93 LEU Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 392 VAL 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 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 296 GLU Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 372 ILE 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 77 GLN 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 431 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 94 optimal weight: 0.0010 chunk 143 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 177 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 115 HIS D 140 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.079203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.061286 restraints weight = 62242.370| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 5.37 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14398 Z= 0.127 Angle : 0.651 10.843 19511 Z= 0.319 Chirality : 0.045 0.206 2219 Planarity : 0.004 0.040 2541 Dihedral : 4.485 51.321 1946 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.22 % Allowed : 14.34 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.20), residues: 1839 helix: 1.73 (0.19), residues: 825 sheet: -0.32 (0.28), residues: 322 loop : -0.88 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.024 0.001 TYR A 382 PHE 0.023 0.001 PHE D 215 TRP 0.049 0.002 TRP B 162 HIS 0.007 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00306 (14398) covalent geometry : angle 0.65057 (19511) hydrogen bonds : bond 0.03235 ( 704) hydrogen bonds : angle 4.95946 ( 2049) *********************** 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 234 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.399 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 158 MET cc_start: 0.8225 (mtm) cc_final: 0.7331 (ttt) REVERT: A 162 TRP cc_start: 0.8213 (m-10) cc_final: 0.7632 (m-10) REVERT: A 176 MET cc_start: 0.9046 (tpt) cc_final: 0.8606 (tpp) REVERT: A 286 MET cc_start: 0.7677 (pmm) cc_final: 0.7372 (pmm) REVERT: B 20 LYS cc_start: 0.9245 (pttm) cc_final: 0.8983 (mmmt) REVERT: B 75 ARG cc_start: 0.9209 (tpm170) cc_final: 0.8916 (tpm170) REVERT: B 158 MET cc_start: 0.8232 (tpt) cc_final: 0.7615 (tpp) REVERT: B 168 MET cc_start: 0.8720 (mmm) cc_final: 0.8505 (mmm) REVERT: B 428 TYR cc_start: 0.9063 (t80) cc_final: 0.8801 (t80) REVERT: B 468 LYS cc_start: 0.3276 (mttt) cc_final: 0.2798 (mttm) REVERT: C 71 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: C 134 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: C 158 MET cc_start: 0.7815 (ttp) cc_final: 0.7017 (tmm) REVERT: C 162 TRP cc_start: 0.8432 (m-10) cc_final: 0.7680 (m-10) REVERT: C 166 MET cc_start: 0.8745 (mmm) cc_final: 0.8320 (mmm) REVERT: D 82 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8417 (tm-30) REVERT: D 90 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9324 (tp) REVERT: D 247 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.7802 (mmt180) REVERT: D 428 TYR cc_start: 0.8756 (t80) cc_final: 0.8408 (t80) outliers start: 49 outliers final: 27 residues processed: 221 average time/residue: 0.1087 time to fit residues: 36.1059 Evaluate side-chains 207 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 452 PHE 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 93 LEU Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 375 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 124 MET 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 D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 77 GLN 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 437 VAL Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 152 optimal weight: 0.0570 chunk 123 optimal weight: 0.0470 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.078394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.060478 restraints weight = 62299.218| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 5.32 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 14398 Z= 0.152 Angle : 0.661 10.234 19511 Z= 0.327 Chirality : 0.045 0.332 2219 Planarity : 0.004 0.041 2541 Dihedral : 4.373 21.228 1944 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.70 % Allowed : 16.58 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.20), residues: 1839 helix: 1.64 (0.19), residues: 830 sheet: -0.33 (0.28), residues: 322 loop : -0.87 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.010 0.001 TYR B 361 PHE 0.021 0.001 PHE A 164 TRP 0.058 0.002 TRP B 162 HIS 0.006 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00362 (14398) covalent geometry : angle 0.66067 (19511) hydrogen bonds : bond 0.03296 ( 704) hydrogen bonds : angle 5.04516 ( 2049) *********************** 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 222 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.659 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: A 15 LYS cc_start: 0.9220 (ptpp) cc_final: 0.8976 (ptpp) REVERT: A 158 MET cc_start: 0.8238 (mtm) cc_final: 0.7344 (ttp) REVERT: A 162 TRP cc_start: 0.8253 (m-10) cc_final: 0.7369 (m-10) REVERT: A 176 MET cc_start: 0.9096 (tpt) cc_final: 0.8870 (tpp) REVERT: A 286 MET cc_start: 0.7671 (pmm) cc_final: 0.7368 (pmm) REVERT: B 20 LYS cc_start: 0.9273 (pttm) cc_final: 0.9026 (mmmt) REVERT: B 70 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8978 (mm-40) REVERT: B 75 ARG cc_start: 0.9211 (tpm170) cc_final: 0.8884 (tpm170) REVERT: B 158 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7645 (tpp) REVERT: B 168 MET cc_start: 0.8817 (mmm) cc_final: 0.8596 (mmm) REVERT: B 293 LEU cc_start: 0.9370 (mt) cc_final: 0.9123 (tp) REVERT: B 428 TYR cc_start: 0.9084 (t80) cc_final: 0.8781 (t80) REVERT: B 468 LYS cc_start: 0.3287 (mttt) cc_final: 0.2779 (mttm) REVERT: C 71 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8714 (mp10) REVERT: C 134 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: C 158 MET cc_start: 0.7813 (ttp) cc_final: 0.6921 (tmm) REVERT: C 162 TRP cc_start: 0.8507 (m-10) cc_final: 0.7671 (m-10) REVERT: C 166 MET cc_start: 0.8772 (mmm) cc_final: 0.8378 (mmm) REVERT: C 246 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8227 (mppt) REVERT: D 90 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9343 (tp) REVERT: D 114 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8598 (mm-30) REVERT: D 168 MET cc_start: 0.8890 (mtp) cc_final: 0.8493 (mmm) REVERT: D 247 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.7805 (mmt180) REVERT: D 261 MET cc_start: 0.6745 (mmt) cc_final: 0.6349 (mmm) REVERT: D 428 TYR cc_start: 0.8808 (t80) cc_final: 0.8457 (t80) outliers start: 41 outliers final: 28 residues processed: 207 average time/residue: 0.1102 time to fit residues: 34.5281 Evaluate side-chains 209 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 452 PHE 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 93 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 375 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 115 HIS 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 D residue 10 LEU Chi-restraints excluded: chain D residue 77 GLN 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 431 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 84 optimal weight: 0.9980 chunk 41 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN 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 = 0.3975 r_free = 0.3975 target = 0.079635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.061547 restraints weight = 61957.233| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 5.51 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14398 Z= 0.122 Angle : 0.656 11.130 19511 Z= 0.320 Chirality : 0.045 0.261 2219 Planarity : 0.004 0.042 2541 Dihedral : 4.255 20.852 1944 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.50 % Allowed : 16.84 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1839 helix: 1.69 (0.19), residues: 831 sheet: -0.43 (0.28), residues: 338 loop : -0.78 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.028 0.001 TYR A 382 PHE 0.024 0.001 PHE A 164 TRP 0.058 0.002 TRP B 162 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00294 (14398) covalent geometry : angle 0.65557 (19511) hydrogen bonds : bond 0.03069 ( 704) hydrogen bonds : angle 4.88034 ( 2049) *********************** 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 226 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.558 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: A 15 LYS cc_start: 0.9251 (ptpp) cc_final: 0.9023 (ptpp) REVERT: A 55 LYS cc_start: 0.9624 (tttt) cc_final: 0.9313 (mttt) REVERT: A 87 ILE cc_start: 0.8908 (mt) cc_final: 0.8678 (tp) REVERT: A 176 MET cc_start: 0.9110 (tpt) cc_final: 0.8902 (tpp) REVERT: A 252 MET cc_start: 0.8117 (mtt) cc_final: 0.7855 (mmm) REVERT: A 286 MET cc_start: 0.7611 (pmm) cc_final: 0.7352 (pmm) REVERT: B 20 LYS cc_start: 0.9322 (pttm) cc_final: 0.9097 (mmmt) REVERT: B 75 ARG cc_start: 0.9223 (tpm170) cc_final: 0.8908 (tpm170) REVERT: B 158 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7488 (mmt) REVERT: B 168 MET cc_start: 0.8871 (mmm) cc_final: 0.8638 (mmm) REVERT: B 267 GLU cc_start: 0.8698 (pm20) cc_final: 0.8055 (pm20) REVERT: B 293 LEU cc_start: 0.9237 (mt) cc_final: 0.8978 (tp) REVERT: B 428 TYR cc_start: 0.9050 (t80) cc_final: 0.8761 (t80) REVERT: B 468 LYS cc_start: 0.3330 (mttt) cc_final: 0.2711 (mttm) REVERT: C 71 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8721 (mp10) REVERT: C 158 MET cc_start: 0.7724 (ttp) cc_final: 0.6898 (tmm) REVERT: C 162 TRP cc_start: 0.8498 (m-10) cc_final: 0.7812 (m-10) REVERT: C 166 MET cc_start: 0.8758 (mmm) cc_final: 0.8382 (mmm) REVERT: C 428 TYR cc_start: 0.9191 (t80) cc_final: 0.8989 (t80) REVERT: D 90 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9348 (tp) REVERT: D 114 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8569 (mm-30) REVERT: D 166 MET cc_start: 0.8806 (tpt) cc_final: 0.8507 (tpp) REVERT: D 168 MET cc_start: 0.8898 (mtp) cc_final: 0.8629 (mmm) REVERT: D 247 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.7807 (mmt180) REVERT: D 261 MET cc_start: 0.6452 (mmt) cc_final: 0.6108 (mmm) REVERT: D 428 TYR cc_start: 0.8681 (t80) cc_final: 0.8255 (t80) REVERT: D 468 LYS cc_start: 0.2509 (mptt) cc_final: 0.2142 (mttt) outliers start: 38 outliers final: 29 residues processed: 213 average time/residue: 0.1090 time to fit residues: 35.3342 Evaluate side-chains 211 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 452 PHE 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 93 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 375 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 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 306 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 77 GLN 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 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 437 VAL 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 115 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 136 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 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 = 0.3946 r_free = 0.3946 target = 0.078174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.060208 restraints weight = 62708.511| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 5.35 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 14398 Z= 0.159 Angle : 0.675 12.092 19511 Z= 0.329 Chirality : 0.045 0.290 2219 Planarity : 0.004 0.043 2541 Dihedral : 4.322 20.993 1944 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.63 % Allowed : 16.91 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.21), residues: 1839 helix: 1.69 (0.19), residues: 831 sheet: -0.46 (0.27), residues: 342 loop : -0.76 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.029 0.002 TYR D 76 PHE 0.018 0.002 PHE A 164 TRP 0.056 0.002 TRP B 162 HIS 0.006 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00381 (14398) covalent geometry : angle 0.67512 (19511) hydrogen bonds : bond 0.03229 ( 704) hydrogen bonds : angle 4.97942 ( 2049) *********************** 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: 40 poor density : 179 time to evaluate : 0.587 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: 0.9255 (ptpp) cc_final: 0.9028 (ptpp) REVERT: A 176 MET cc_start: 0.9116 (tpt) cc_final: 0.8877 (tpp) REVERT: A 252 MET cc_start: 0.8206 (mtt) cc_final: 0.7913 (mmm) REVERT: A 286 MET cc_start: 0.7655 (pmm) cc_final: 0.7382 (pmm) REVERT: B 20 LYS cc_start: 0.9341 (pttm) cc_final: 0.9117 (mmmt) REVERT: B 75 ARG cc_start: 0.9232 (tpm170) cc_final: 0.8931 (tpm170) REVERT: B 76 TYR cc_start: 0.9583 (t80) cc_final: 0.9330 (t80) REVERT: B 158 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7475 (mmt) REVERT: B 168 MET cc_start: 0.8945 (mmm) cc_final: 0.8598 (mmm) REVERT: B 255 LYS cc_start: 0.8478 (mmtt) cc_final: 0.7682 (mmtt) REVERT: B 293 LEU cc_start: 0.9289 (mt) cc_final: 0.9027 (tp) REVERT: B 428 TYR cc_start: 0.9105 (t80) cc_final: 0.8797 (t80) REVERT: B 468 LYS cc_start: 0.3121 (mttt) cc_final: 0.2405 (mttm) REVERT: C 71 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: C 166 MET cc_start: 0.8811 (mmm) cc_final: 0.8408 (mmm) REVERT: C 428 TYR cc_start: 0.9262 (t80) cc_final: 0.9048 (t80) REVERT: D 90 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9352 (tp) REVERT: D 114 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8637 (mm-30) REVERT: D 166 MET cc_start: 0.8925 (tpt) cc_final: 0.8583 (tpp) REVERT: D 168 MET cc_start: 0.8873 (mtp) cc_final: 0.8612 (mmm) REVERT: D 247 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.7815 (mmt180) REVERT: D 261 MET cc_start: 0.6662 (mmt) cc_final: 0.6286 (mmm) REVERT: D 428 TYR cc_start: 0.8751 (t80) cc_final: 0.8006 (t80) outliers start: 40 outliers final: 33 residues processed: 207 average time/residue: 0.1073 time to fit residues: 33.4160 Evaluate side-chains 214 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL 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 361 TYR Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 375 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 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 306 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 77 GLN 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 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 437 VAL 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 87 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 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 = 0.3953 r_free = 0.3953 target = 0.078690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.060728 restraints weight = 62454.363| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 5.36 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14398 Z= 0.134 Angle : 0.688 14.404 19511 Z= 0.332 Chirality : 0.045 0.256 2219 Planarity : 0.004 0.046 2541 Dihedral : 4.282 20.749 1944 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.50 % Allowed : 17.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.21), residues: 1839 helix: 1.68 (0.19), residues: 831 sheet: -0.45 (0.28), residues: 342 loop : -0.74 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.028 0.001 TYR D 76 PHE 0.020 0.001 PHE A 164 TRP 0.056 0.002 TRP B 162 HIS 0.006 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00323 (14398) covalent geometry : angle 0.68781 (19511) hydrogen bonds : bond 0.03173 ( 704) hydrogen bonds : angle 4.95239 ( 2049) ********************** 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 220 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.398 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: 0.9255 (ptpp) cc_final: 0.9028 (ptpp) REVERT: A 55 LYS cc_start: 0.9618 (tttt) cc_final: 0.9367 (mttt) REVERT: A 87 ILE cc_start: 0.8887 (mt) cc_final: 0.8662 (tp) REVERT: A 158 MET cc_start: 0.8547 (ttp) cc_final: 0.8321 (ptm) REVERT: A 176 MET cc_start: 0.9145 (tpt) cc_final: 0.8925 (tpp) REVERT: A 252 MET cc_start: 0.8323 (mtt) cc_final: 0.8009 (mmm) REVERT: A 286 MET cc_start: 0.7634 (pmm) cc_final: 0.7370 (pmm) REVERT: A 472 GLN cc_start: 0.8918 (mt0) cc_final: 0.8594 (mt0) REVERT: B 20 LYS cc_start: 0.9335 (pttm) cc_final: 0.9110 (mmmt) REVERT: B 75 ARG cc_start: 0.9225 (tpm170) cc_final: 0.8902 (tpm170) REVERT: B 76 TYR cc_start: 0.9574 (t80) cc_final: 0.9323 (t80) REVERT: B 158 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7404 (mmt) REVERT: B 168 MET cc_start: 0.8929 (mmm) cc_final: 0.8579 (mmm) REVERT: B 255 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7779 (mmtt) REVERT: B 267 GLU cc_start: 0.8674 (pm20) cc_final: 0.8030 (pm20) REVERT: B 293 LEU cc_start: 0.9278 (mt) cc_final: 0.9009 (tp) REVERT: B 428 TYR cc_start: 0.9093 (t80) cc_final: 0.8799 (t80) REVERT: B 468 LYS cc_start: 0.3050 (mttt) cc_final: 0.2443 (mttm) REVERT: C 71 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8768 (mp10) REVERT: C 166 MET cc_start: 0.8772 (mmm) cc_final: 0.8368 (mmm) REVERT: C 428 TYR cc_start: 0.9259 (t80) cc_final: 0.9025 (t80) REVERT: D 90 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9338 (tp) REVERT: D 114 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8565 (mm-30) REVERT: D 158 MET cc_start: 0.7359 (tpt) cc_final: 0.6961 (tpt) REVERT: D 166 MET cc_start: 0.8902 (tpt) cc_final: 0.8577 (tpp) REVERT: D 168 MET cc_start: 0.8868 (mtp) cc_final: 0.8631 (mmm) REVERT: D 247 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.7804 (mmt180) REVERT: D 261 MET cc_start: 0.6532 (mmt) cc_final: 0.6161 (mmm) REVERT: D 428 TYR cc_start: 0.8726 (t80) cc_final: 0.7996 (t80) REVERT: D 468 LYS cc_start: 0.2658 (mptt) cc_final: 0.2290 (mttt) outliers start: 38 outliers final: 32 residues processed: 207 average time/residue: 0.0965 time to fit residues: 30.2822 Evaluate side-chains 216 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL 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 361 TYR 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 73 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 375 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 186 THR Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 77 GLN 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 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 437 VAL 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 112 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN B 430 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 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 = 0.3924 r_free = 0.3924 target = 0.077125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.059224 restraints weight = 62922.391| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.29 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 14398 Z= 0.195 Angle : 0.718 13.282 19511 Z= 0.354 Chirality : 0.045 0.283 2219 Planarity : 0.004 0.044 2541 Dihedral : 4.462 20.896 1944 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.63 % Allowed : 17.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1839 helix: 1.65 (0.19), residues: 829 sheet: -0.47 (0.28), residues: 342 loop : -0.79 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.015 0.002 TYR B 474 PHE 0.035 0.002 PHE C 155 TRP 0.054 0.002 TRP B 162 HIS 0.009 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00460 (14398) covalent geometry : angle 0.71781 (19511) hydrogen bonds : bond 0.03494 ( 704) hydrogen bonds : angle 5.14366 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.07 seconds wall clock time: 52 minutes 1.21 seconds (3121.21 seconds total)