Starting phenix.real_space_refine on Mon Dec 30 20:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izv_61043/12_2024/9izv_61043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izv_61043/12_2024/9izv_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_61043/12_2024/9izv_61043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izv_61043/12_2024/9izv_61043.map" model { file = "/net/cci-nas-00/data/ceres_data/9izv_61043/12_2024/9izv_61043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izv_61043/12_2024/9izv_61043.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 8961 2.51 5 N 2445 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3695 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 27, 'TRANS': 457} Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3320 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 26, 'TRANS': 412} Chain breaks: 2 Chain: "C" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3580 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 27, 'TRANS': 442} Chain breaks: 1 Chain: "D" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3523 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 26, 'TRANS': 436} Chain breaks: 2 Time building chain proxies: 8.80, per 1000 atoms: 0.62 Number of scatterers: 14118 At special positions: 0 Unit cell: (111.24, 119.48, 115.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2621 8.00 N 2445 7.00 C 8961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 48.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 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: 5.97 Time building geometry restraints manager: 4.06 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.310 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 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:3.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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= 0.140 Angle : 0.485 11.714 19511 Z= 0.275 Chirality : 0.042 0.325 2219 Planarity : 0.003 0.042 2541 Dihedral : 8.208 79.968 5328 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.20 % Allowed : 3.22 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1839 helix: 0.97 (0.17), residues: 807 sheet: -0.99 (0.26), residues: 318 loop : -1.92 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 484 HIS 0.002 0.000 HIS C 244 PHE 0.020 0.001 PHE A 459 TYR 0.007 0.001 TYR A 236 ARG 0.002 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.7831 (mtm) cc_final: 0.7471 (mtm) REVERT: C 67 LEU cc_start: 0.8007 (mt) cc_final: 0.7260 (mp) REVERT: C 158 MET cc_start: 0.5848 (ttp) cc_final: 0.5336 (tmm) REVERT: C 168 MET cc_start: 0.7622 (mmt) cc_final: 0.7329 (mmt) REVERT: D 468 LYS cc_start: 0.2109 (mptt) cc_final: 0.1196 (mttt) outliers start: 3 outliers final: 2 residues processed: 412 average time/residue: 0.3218 time to fit residues: 183.7533 Evaluate side-chains 229 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 231 ASN A 318 GLN A 374 ASN A 404 GLN A 472 GLN B 78 GLN B 115 HIS B 194 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 283 GLN B 318 GLN B 476 GLN C 41 GLN C 78 GLN C 95 GLN C 207 HIS C 310 ASN C 318 GLN C 365 ASN C 430 HIS C 436 GLN C 472 GLN D 33 ASN D 95 GLN D 256 ASN D 318 GLN D 413 ASN D 472 GLN D 483 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.199 14398 Z= 0.489 Angle : 0.814 10.849 19511 Z= 0.417 Chirality : 0.049 0.203 2219 Planarity : 0.006 0.054 2541 Dihedral : 4.896 44.049 1948 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 3.49 % Allowed : 12.04 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1839 helix: 1.02 (0.17), residues: 824 sheet: -0.46 (0.27), residues: 318 loop : -1.43 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 162 HIS 0.012 0.002 HIS C 219 PHE 0.018 0.002 PHE C 418 TYR 0.023 0.003 TYR B 76 ARG 0.008 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7560 (mt) cc_final: 0.7283 (tp) REVERT: A 449 MET cc_start: 0.6215 (tmm) cc_final: 0.5924 (ptm) REVERT: B 317 ASP cc_start: 0.7078 (p0) cc_final: 0.6411 (p0) REVERT: B 468 LYS cc_start: 0.2474 (mttp) cc_final: 0.1865 (mttt) REVERT: D 449 MET cc_start: 0.2368 (OUTLIER) cc_final: 0.2159 (ttt) REVERT: D 468 LYS cc_start: 0.2229 (mptt) cc_final: 0.1676 (mttp) outliers start: 53 outliers final: 33 residues processed: 238 average time/residue: 0.2700 time to fit residues: 94.9427 Evaluate side-chains 194 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 300 TRP Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 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 92 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 14398 Z= 0.277 Angle : 0.680 12.543 19511 Z= 0.339 Chirality : 0.046 0.279 2219 Planarity : 0.004 0.039 2541 Dihedral : 4.778 51.368 1948 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.22 % Allowed : 13.16 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1839 helix: 1.37 (0.18), residues: 823 sheet: -0.31 (0.27), residues: 329 loop : -1.18 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 300 HIS 0.007 0.001 HIS B 115 PHE 0.022 0.002 PHE A 164 TYR 0.032 0.002 TYR B 411 ARG 0.004 0.001 ARG D 108 *********************** 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 233 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 1.621 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: A 87 ILE cc_start: 0.7509 (mt) cc_final: 0.7302 (tp) REVERT: B 47 MET cc_start: 0.7485 (mtm) cc_final: 0.7137 (mtm) REVERT: B 468 LYS cc_start: 0.2257 (mttp) cc_final: 0.1616 (mttt) outliers start: 49 outliers final: 32 residues processed: 222 average time/residue: 0.2766 time to fit residues: 88.8842 Evaluate side-chains 198 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 115 HIS B 207 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS C 41 GLN C 209 GLN D 77 GLN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 14398 Z= 0.261 Angle : 0.667 11.957 19511 Z= 0.333 Chirality : 0.046 0.191 2219 Planarity : 0.004 0.039 2541 Dihedral : 4.894 57.084 1948 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.95 % Allowed : 13.36 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1839 helix: 1.47 (0.18), residues: 823 sheet: -0.32 (0.28), residues: 331 loop : -1.07 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 162 HIS 0.007 0.001 HIS B 115 PHE 0.018 0.002 PHE A 164 TYR 0.025 0.002 TYR B 411 ARG 0.004 0.000 ARG A 284 *********************** 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 244 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 1.618 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: B 468 LYS cc_start: 0.2291 (mttp) cc_final: 0.1704 (mttt) REVERT: C 158 MET cc_start: 0.6486 (tmm) cc_final: 0.5307 (tmm) outliers start: 60 outliers final: 39 residues processed: 230 average time/residue: 0.2546 time to fit residues: 87.0899 Evaluate side-chains 207 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 403 ILE 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 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 159 optimal weight: 0.0980 chunk 44 optimal weight: 20.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 207 HIS B 430 HIS C 41 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 14398 Z= 0.329 Angle : 0.716 12.265 19511 Z= 0.358 Chirality : 0.046 0.346 2219 Planarity : 0.005 0.042 2541 Dihedral : 4.818 48.531 1946 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.88 % Allowed : 14.54 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1839 helix: 1.42 (0.18), residues: 823 sheet: -0.29 (0.28), residues: 326 loop : -0.99 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 162 HIS 0.011 0.001 HIS B 115 PHE 0.017 0.002 PHE A 164 TYR 0.027 0.002 TYR B 411 ARG 0.006 0.001 ARG B 75 *********************** 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 229 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 1.696 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: A 73 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7708 (tp) REVERT: B 468 LYS cc_start: 0.2279 (mttp) cc_final: 0.1764 (mttm) outliers start: 59 outliers final: 42 residues processed: 216 average time/residue: 0.2484 time to fit residues: 81.5644 Evaluate side-chains 207 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 107 PHE 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 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 333 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS C 41 GLN D 307 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 14398 Z= 0.281 Angle : 0.694 13.256 19511 Z= 0.343 Chirality : 0.046 0.213 2219 Planarity : 0.004 0.041 2541 Dihedral : 4.813 49.390 1946 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.88 % Allowed : 15.00 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1839 helix: 1.48 (0.18), residues: 823 sheet: -0.28 (0.28), residues: 328 loop : -0.98 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 162 HIS 0.007 0.001 HIS C 219 PHE 0.025 0.002 PHE A 164 TYR 0.024 0.002 TYR A 382 ARG 0.004 0.000 ARG B 75 *********************** 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 236 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 1.574 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 73 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7683 (tp) REVERT: B 76 TYR cc_start: 0.7948 (t80) cc_final: 0.7649 (t80) REVERT: B 468 LYS cc_start: 0.2313 (mttp) cc_final: 0.1827 (mttm) REVERT: C 158 MET cc_start: 0.6388 (tmm) cc_final: 0.5102 (tmm) outliers start: 59 outliers final: 41 residues processed: 223 average time/residue: 0.2478 time to fit residues: 83.1235 Evaluate side-chains 211 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 107 PHE 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 134 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 300 TRP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 14398 Z= 0.273 Angle : 0.693 13.920 19511 Z= 0.344 Chirality : 0.046 0.217 2219 Planarity : 0.004 0.043 2541 Dihedral : 4.807 50.094 1946 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.55 % Allowed : 15.92 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1839 helix: 1.46 (0.18), residues: 824 sheet: -0.28 (0.28), residues: 329 loop : -0.96 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 162 HIS 0.007 0.001 HIS C 219 PHE 0.016 0.002 PHE C 155 TYR 0.013 0.001 TYR B 411 ARG 0.003 0.000 ARG A 284 *********************** 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 236 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.8133 (t80) cc_final: 0.7752 (t80) REVERT: B 468 LYS cc_start: 0.2339 (mttp) cc_final: 0.1776 (mttm) REVERT: C 158 MET cc_start: 0.6553 (tmm) cc_final: 0.5634 (tmm) outliers start: 54 outliers final: 41 residues processed: 222 average time/residue: 0.2518 time to fit residues: 83.7226 Evaluate side-chains 207 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 ILE 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 134 ASP Chi-restraints excluded: chain C residue 155 PHE 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 333 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 14398 Z= 0.342 Angle : 0.757 15.038 19511 Z= 0.375 Chirality : 0.047 0.370 2219 Planarity : 0.005 0.044 2541 Dihedral : 4.987 50.678 1946 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.82 % Allowed : 16.45 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1839 helix: 1.37 (0.18), residues: 825 sheet: -0.51 (0.27), residues: 346 loop : -0.99 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP B 162 HIS 0.008 0.001 HIS C 219 PHE 0.023 0.002 PHE A 465 TYR 0.027 0.002 TYR A 382 ARG 0.008 0.001 ARG C 354 *********************** 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 228 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.708 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: B 76 TYR cc_start: 0.8173 (t80) cc_final: 0.7873 (t80) REVERT: B 468 LYS cc_start: 0.2395 (mttp) cc_final: 0.1697 (mttt) outliers start: 58 outliers final: 48 residues processed: 212 average time/residue: 0.2480 time to fit residues: 79.5618 Evaluate side-chains 214 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 155 PHE 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 333 GLU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS C 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 14398 Z= 0.279 Angle : 0.759 16.211 19511 Z= 0.374 Chirality : 0.047 0.332 2219 Planarity : 0.005 0.057 2541 Dihedral : 4.935 51.753 1946 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.55 % Allowed : 16.78 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1839 helix: 1.42 (0.18), residues: 831 sheet: -0.49 (0.27), residues: 348 loop : -0.97 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.004 TRP B 162 HIS 0.007 0.001 HIS C 219 PHE 0.017 0.002 PHE C 155 TYR 0.027 0.002 TYR A 382 ARG 0.008 0.001 ARG C 354 *********************** 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 224 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 LYS cc_start: 0.2359 (mttp) cc_final: 0.1787 (mttm) REVERT: D 484 TRP cc_start: 0.3772 (OUTLIER) cc_final: 0.2993 (m-10) outliers start: 54 outliers final: 44 residues processed: 212 average time/residue: 0.2549 time to fit residues: 82.0222 Evaluate side-chains 209 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 155 PHE 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 333 GLU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 14398 Z= 0.274 Angle : 0.780 17.281 19511 Z= 0.385 Chirality : 0.047 0.329 2219 Planarity : 0.005 0.054 2541 Dihedral : 4.979 52.507 1946 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.22 % Allowed : 17.11 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1839 helix: 1.39 (0.18), residues: 826 sheet: -0.37 (0.28), residues: 334 loop : -0.92 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.004 TRP A 162 HIS 0.008 0.001 HIS B 115 PHE 0.032 0.002 PHE A 164 TYR 0.052 0.002 TYR B 76 ARG 0.008 0.001 ARG C 354 ********************** 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 217 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 LYS cc_start: 0.2319 (mttp) cc_final: 0.1759 (mttm) REVERT: C 168 MET cc_start: 0.8066 (mmm) cc_final: 0.7477 (mmt) REVERT: D 484 TRP cc_start: 0.3744 (OUTLIER) cc_final: 0.3038 (m-10) outliers start: 49 outliers final: 43 residues processed: 206 average time/residue: 0.2502 time to fit residues: 77.8329 Evaluate side-chains 206 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 155 PHE 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 333 GLU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 117 CYS Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.077325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.059505 restraints weight = 63599.546| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 5.30 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5473 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= 0.252 Angle : 0.783 16.678 19511 Z= 0.385 Chirality : 0.047 0.319 2219 Planarity : 0.005 0.050 2541 Dihedral : 4.920 53.430 1946 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.16 % Allowed : 16.97 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1839 helix: 1.42 (0.18), residues: 825 sheet: -0.46 (0.28), residues: 346 loop : -0.90 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.004 TRP A 162 HIS 0.006 0.001 HIS A 219 PHE 0.018 0.002 PHE C 164 TYR 0.023 0.002 TYR B 76 ARG 0.007 0.001 ARG C 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.69 seconds wall clock time: 53 minutes 16.20 seconds (3196.20 seconds total)