Starting phenix.real_space_refine on Sat Jan 18 11:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtq_47156/01_2025/9dtq_47156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtq_47156/01_2025/9dtq_47156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dtq_47156/01_2025/9dtq_47156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtq_47156/01_2025/9dtq_47156.map" model { file = "/net/cci-nas-00/data/ceres_data/9dtq_47156/01_2025/9dtq_47156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtq_47156/01_2025/9dtq_47156.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 75 5.16 5 C 7706 2.51 5 N 2079 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12162 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2960 Classifications: {'peptide': 367} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 350} Chain: "B" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4041 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 16, 'TRANS': 494} Chain: "D" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1068 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 4057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4057 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 497} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.12, per 1000 atoms: 0.67 Number of scatterers: 12162 At special positions: 0 Unit cell: (77.28, 128.52, 161.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 6 15.00 O 2296 8.00 N 2079 7.00 C 7706 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 23 sheets defined 37.7% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.826A pdb=" N TYR A 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.692A pdb=" N MET A 52 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.975A pdb=" N MET A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 106 through 127 removed outlier: 3.585A pdb=" N SER A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.642A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.706A pdb=" N LYS A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 263 through 267 removed outlier: 4.253A pdb=" N SER A 266 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 267 " --> pdb=" O ALA A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 278 through 290 removed outlier: 4.382A pdb=" N CYS A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 286 " --> pdb=" O HIS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 305 through 321 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.830A pdb=" N GLY A 339 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'B' and resid 41 through 56 removed outlier: 3.512A pdb=" N GLU B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.517A pdb=" N THR B 188 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.566A pdb=" N LEU B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 4.255A pdb=" N ASN B 232 " --> pdb=" O TRP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 475 through 479 removed outlier: 4.099A pdb=" N TRP B 478 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 57 removed outlier: 3.567A pdb=" N HIS D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.794A pdb=" N ALA D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 92 through 107 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.682A pdb=" N GLN D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'E' and resid 41 through 56 Processing helix chain 'E' and resid 75 through 83 Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.512A pdb=" N ARG E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 92 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 143 through 157 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.554A pdb=" N HIS E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 Processing helix chain 'E' and resid 189 through 195 removed outlier: 4.482A pdb=" N ASN E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.734A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 196 through 201' Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.630A pdb=" N ASP E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 removed outlier: 3.796A pdb=" N ASN E 232 " --> pdb=" O TRP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.586A pdb=" N GLU E 237 " --> pdb=" O LYS E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 408 through 410 No H-bonds generated for 'chain 'E' and resid 408 through 410' Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 229 removed outlier: 8.056A pdb=" N VAL A 225 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE A 227 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER A 198 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET A 229 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N HIS A 200 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 171 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 197 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A 173 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE A 199 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP A 175 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LYS A 201 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 258 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU A 299 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 260 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 133 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS A 13 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 54 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 74 Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 127 Processing sheet with id=AA5, first strand: chain 'B' and resid 215 through 216 removed outlier: 7.075A pdb=" N VAL B 215 " --> pdb=" O ILE B 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.605A pdb=" N ALA B 270 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B 286 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N SER B 272 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 297 removed outlier: 4.230A pdb=" N GLN B 292 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 306 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 296 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR B 304 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 344 removed outlier: 5.439A pdb=" N ALA B 365 " --> pdb=" O GLY B 354 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS B 356 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER B 363 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 375 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 390 through 393 removed outlier: 5.021A pdb=" N ILE B 418 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AB3, first strand: chain 'B' and resid 441 through 446 removed outlier: 3.823A pdb=" N ALA B 454 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 459 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 485 through 490 removed outlier: 4.444A pdb=" N THR B 508 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 517 " --> pdb=" O ASP B 512 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 70 through 74 Processing sheet with id=AB6, first strand: chain 'E' and resid 215 through 216 removed outlier: 6.508A pdb=" N VAL E 215 " --> pdb=" O ILE E 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 281 through 289 removed outlier: 5.345A pdb=" N VAL E 283 " --> pdb=" O HIS E 274 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS E 274 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS E 261 " --> pdb=" O LEU E 531 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU E 531 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 293 through 299 removed outlier: 5.996A pdb=" N ILE E 293 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY E 308 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL E 305 " --> pdb=" O MET E 316 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N MET E 316 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY E 307 " --> pdb=" O ARG E 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 309 " --> pdb=" O ARG E 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AC1, first strand: chain 'E' and resid 340 through 344 removed outlier: 4.547A pdb=" N VAL E 366 " --> pdb=" O THR E 379 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 370 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL E 375 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 386 through 387 removed outlier: 3.719A pdb=" N PHE E 411 " --> pdb=" O ASP E 407 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 390 through 393 removed outlier: 3.594A pdb=" N LYS E 427 " --> pdb=" O ASP E 422 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 442 through 445 Processing sheet with id=AC5, first strand: chain 'E' and resid 485 through 490 removed outlier: 3.628A pdb=" N ALA E 517 " --> pdb=" O ASP E 512 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 3.41 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: 2807 1.33 - 1.45: 2691 1.45 - 1.57: 6830 1.57 - 1.69: 6 1.69 - 1.81: 109 Bond restraints: 12443 Sorted by residual: bond pdb=" C5 IHP D 401 " pdb=" O15 IHP D 401 " ideal model delta sigma weight residual 1.389 1.443 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C3 IHP D 401 " pdb=" O13 IHP D 401 " ideal model delta sigma weight residual 1.393 1.444 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C1 IHP D 401 " pdb=" O11 IHP D 401 " ideal model delta sigma weight residual 1.392 1.443 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C4 IHP D 401 " pdb=" O14 IHP D 401 " ideal model delta sigma weight residual 1.394 1.444 -0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" O16 IHP D 401 " pdb=" P6 IHP D 401 " ideal model delta sigma weight residual 1.672 1.622 0.050 2.00e-02 2.50e+03 6.18e+00 ... (remaining 12438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 16756 2.62 - 5.25: 97 5.25 - 7.87: 15 7.87 - 10.50: 1 10.50 - 13.12: 2 Bond angle restraints: 16871 Sorted by residual: angle pdb=" N THR E 470 " pdb=" CA THR E 470 " pdb=" C THR E 470 " ideal model delta sigma weight residual 109.50 101.85 7.65 1.58e+00 4.01e-01 2.34e+01 angle pdb=" C3 IHP D 401 " pdb=" O13 IHP D 401 " pdb=" P3 IHP D 401 " ideal model delta sigma weight residual 118.69 131.81 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" N VAL D 33 " pdb=" CA VAL D 33 " pdb=" C VAL D 33 " ideal model delta sigma weight residual 112.96 109.25 3.71 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA THR E 470 " pdb=" C THR E 470 " pdb=" O THR E 470 " ideal model delta sigma weight residual 121.11 116.90 4.21 1.17e+00 7.31e-01 1.30e+01 angle pdb=" C1 IHP D 401 " pdb=" O11 IHP D 401 " pdb=" P1 IHP D 401 " ideal model delta sigma weight residual 118.92 129.60 -10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 16866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.86: 6847 28.86 - 57.71: 537 57.71 - 86.57: 34 86.57 - 115.43: 12 115.43 - 144.29: 3 Dihedral angle restraints: 7433 sinusoidal: 2989 harmonic: 4444 Sorted by residual: dihedral pdb=" CA LEU E 408 " pdb=" C LEU E 408 " pdb=" N ASP E 409 " pdb=" CA ASP E 409 " ideal model delta harmonic sigma weight residual -180.00 -135.69 -44.31 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CD ARG E 471 " pdb=" NE ARG E 471 " pdb=" CZ ARG E 471 " pdb=" NH1 ARG E 471 " ideal model delta sinusoidal sigma weight residual 0.00 -40.00 40.00 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA ASP E 409 " pdb=" C ASP E 409 " pdb=" N PHE E 410 " pdb=" CA PHE E 410 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1848 1.009 - 2.017: 0 2.017 - 3.026: 0 3.026 - 4.035: 0 4.035 - 5.043: 2 Chirality restraints: 1850 Sorted by residual: chirality pdb=" C4 IHP D 401 " pdb=" C3 IHP D 401 " pdb=" C5 IHP D 401 " pdb=" O14 IHP D 401 " both_signs ideal model delta sigma weight residual False 2.48 -2.56 5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C3 IHP D 401 " pdb=" C2 IHP D 401 " pdb=" C4 IHP D 401 " pdb=" O13 IHP D 401 " both_signs ideal model delta sigma weight residual False -2.34 2.54 -4.88 2.00e-01 2.50e+01 5.96e+02 chirality pdb=" C1 IHP D 401 " pdb=" C2 IHP D 401 " pdb=" C6 IHP D 401 " pdb=" O11 IHP D 401 " both_signs ideal model delta sigma weight residual False 2.32 2.57 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1847 not shown) Planarity restraints: 2170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 471 " 0.705 9.50e-02 1.11e+02 3.16e-01 6.08e+01 pdb=" NE ARG E 471 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG E 471 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 471 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 471 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 310 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO E 311 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 58 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C GLU E 58 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU E 58 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU E 59 " -0.009 2.00e-02 2.50e+03 ... (remaining 2167 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 572 2.73 - 3.27: 11314 3.27 - 3.82: 19584 3.82 - 4.36: 24504 4.36 - 4.90: 42794 Nonbonded interactions: 98768 Sorted by model distance: nonbonded pdb=" OD2 ASP A 235 " pdb=" OG1 THR A 278 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR B 433 " pdb=" OD1 ASP B 467 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR B 369 " pdb=" OD1 ASN B 374 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU B 57 " pdb=" NH2 ARG E 87 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR E 433 " pdb=" OD1 ASP E 467 " model vdw 2.279 3.040 ... (remaining 98763 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 'B' selection = (chain 'E' and resid 26 through 536) } 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: 6.430 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.660 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12443 Z= 0.206 Angle : 0.545 13.120 16871 Z= 0.281 Chirality : 0.169 5.043 1850 Planarity : 0.008 0.316 2170 Dihedral : 18.950 144.286 4573 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 4.08 % Allowed : 27.62 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.06 (0.21), residues: 1512 helix: 0.87 (0.23), residues: 491 sheet: 0.53 (0.28), residues: 359 loop : -1.03 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.014 0.001 HIS B 204 PHE 0.011 0.001 PHE E 437 TYR 0.016 0.001 TYR A 304 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7491 (t0) cc_final: 0.7144 (m-30) REVERT: A 75 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7773 (mtpp) REVERT: A 298 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8330 (mtm) REVERT: B 38 LYS cc_start: 0.8806 (ttpp) cc_final: 0.7713 (tptt) REVERT: B 50 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7153 (mp) REVERT: B 51 MET cc_start: 0.7297 (mtp) cc_final: 0.6893 (mtt) REVERT: B 65 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7606 (mm) REVERT: B 87 ARG cc_start: 0.7473 (ttm170) cc_final: 0.6440 (tmt170) REVERT: B 91 THR cc_start: 0.7800 (m) cc_final: 0.7459 (p) REVERT: B 100 ARG cc_start: 0.4466 (OUTLIER) cc_final: 0.3803 (mmm160) REVERT: B 255 HIS cc_start: 0.7204 (OUTLIER) cc_final: 0.6479 (t-90) REVERT: B 275 CYS cc_start: 0.7445 (m) cc_final: 0.7229 (t) REVERT: B 335 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7064 (p0) REVERT: B 404 GLU cc_start: 0.7666 (tp30) cc_final: 0.7319 (tt0) REVERT: B 440 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7221 (ptm-80) REVERT: B 528 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6655 (mp) REVERT: B 530 ASN cc_start: 0.8123 (m-40) cc_final: 0.7720 (t0) REVERT: D 75 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: E 48 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: E 51 MET cc_start: 0.7051 (mtp) cc_final: 0.6651 (mtt) REVERT: E 174 SER cc_start: 0.7606 (m) cc_final: 0.7302 (t) REVERT: E 190 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6587 (tt) REVERT: E 211 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6566 (mp) REVERT: E 212 SER cc_start: 0.7271 (t) cc_final: 0.6880 (p) REVERT: E 220 ASN cc_start: 0.6637 (m-40) cc_final: 0.6319 (t0) REVERT: E 311 PRO cc_start: 0.7206 (Cg_endo) cc_final: 0.6946 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7220 (ptp90) REVERT: E 401 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8252 (mt) REVERT: E 429 HIS cc_start: 0.7500 (m90) cc_final: 0.7249 (m90) REVERT: E 473 CYS cc_start: 0.8223 (m) cc_final: 0.8017 (m) outliers start: 54 outliers final: 34 residues processed: 186 average time/residue: 1.3677 time to fit residues: 274.7879 Evaluate side-chains 186 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 194 GLN B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 320 ASN E 321 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.179479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122849 restraints weight = 12174.096| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.34 r_work: 0.3184 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12443 Z= 0.247 Angle : 0.567 8.112 16871 Z= 0.293 Chirality : 0.045 0.260 1850 Planarity : 0.004 0.040 2170 Dihedral : 10.232 90.236 1789 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 5.58 % Allowed : 24.83 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.01 (0.21), residues: 1512 helix: 0.95 (0.23), residues: 511 sheet: 0.63 (0.28), residues: 356 loop : -1.12 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.006 0.001 HIS B 204 PHE 0.013 0.001 PHE E 437 TYR 0.017 0.002 TYR B 135 ARG 0.003 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7449 (t0) cc_final: 0.6975 (m-30) REVERT: A 290 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7380 (mtpp) REVERT: B 38 LYS cc_start: 0.8792 (ttpp) cc_final: 0.7637 (tptt) REVERT: B 50 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6729 (mp) REVERT: B 51 MET cc_start: 0.7133 (mtp) cc_final: 0.6648 (mtt) REVERT: B 87 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6205 (tmt170) REVERT: B 255 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6680 (t-90) REVERT: B 275 CYS cc_start: 0.7538 (m) cc_final: 0.6819 (t) REVERT: B 335 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7055 (p0) REVERT: B 404 GLU cc_start: 0.7861 (tp30) cc_final: 0.7343 (tt0) REVERT: B 505 ASP cc_start: 0.1291 (OUTLIER) cc_final: 0.1080 (m-30) REVERT: B 528 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6531 (mp) REVERT: B 530 ASN cc_start: 0.7636 (m-40) cc_final: 0.7162 (t0) REVERT: E 48 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6565 (mp10) REVERT: E 51 MET cc_start: 0.6907 (mtp) cc_final: 0.6438 (mtt) REVERT: E 174 SER cc_start: 0.7415 (m) cc_final: 0.7159 (t) REVERT: E 190 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6380 (tt) REVERT: E 192 GLN cc_start: 0.5996 (mt0) cc_final: 0.5650 (tt0) REVERT: E 211 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6463 (mp) REVERT: E 212 SER cc_start: 0.7176 (t) cc_final: 0.6824 (p) REVERT: E 310 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7055 (tt) REVERT: E 311 PRO cc_start: 0.7165 (Cg_endo) cc_final: 0.6822 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7780 (ptm-80) cc_final: 0.7093 (ptp90) REVERT: E 401 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8161 (mt) REVERT: E 429 HIS cc_start: 0.7351 (m90) cc_final: 0.6976 (m90) REVERT: E 473 CYS cc_start: 0.8350 (m) cc_final: 0.8141 (m) outliers start: 74 outliers final: 25 residues processed: 208 average time/residue: 1.3083 time to fit residues: 295.9099 Evaluate side-chains 177 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 91 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 230 ASN B 292 GLN E 184 HIS E 192 GLN E 201 HIS E 286 GLN E 320 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.180273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130089 restraints weight = 12435.598| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.58 r_work: 0.3177 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12443 Z= 0.202 Angle : 0.524 7.641 16871 Z= 0.271 Chirality : 0.044 0.255 1850 Planarity : 0.003 0.036 2170 Dihedral : 9.151 89.917 1742 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 5.58 % Allowed : 25.74 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.12 (0.21), residues: 1512 helix: 1.22 (0.23), residues: 504 sheet: 0.60 (0.28), residues: 356 loop : -1.13 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 PHE 0.012 0.001 PHE E 437 TYR 0.016 0.001 TYR A 304 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7337 (t0) cc_final: 0.6990 (m-30) REVERT: A 75 LYS cc_start: 0.7695 (ttpp) cc_final: 0.7381 (mtpp) REVERT: A 290 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7421 (mtpp) REVERT: B 38 LYS cc_start: 0.8736 (ttpp) cc_final: 0.7551 (tptt) REVERT: B 50 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6767 (mp) REVERT: B 51 MET cc_start: 0.7099 (mtp) cc_final: 0.6634 (mtt) REVERT: B 87 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6260 (tmt170) REVERT: B 255 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6684 (t-90) REVERT: B 275 CYS cc_start: 0.7498 (m) cc_final: 0.6942 (t) REVERT: B 335 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7059 (p0) REVERT: B 404 GLU cc_start: 0.7706 (tp30) cc_final: 0.7378 (tt0) REVERT: B 440 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7133 (ptm-80) REVERT: B 505 ASP cc_start: 0.1507 (OUTLIER) cc_final: 0.1298 (m-30) REVERT: B 528 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6489 (mp) REVERT: B 530 ASN cc_start: 0.7637 (m-40) cc_final: 0.7209 (t0) REVERT: D 75 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: E 51 MET cc_start: 0.6891 (mtp) cc_final: 0.6471 (mtt) REVERT: E 190 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6401 (tt) REVERT: E 192 GLN cc_start: 0.6013 (mt0) cc_final: 0.5643 (tt0) REVERT: E 209 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6124 (m-30) REVERT: E 211 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6457 (mp) REVERT: E 212 SER cc_start: 0.7162 (t) cc_final: 0.6834 (p) REVERT: E 213 ASP cc_start: 0.5584 (OUTLIER) cc_final: 0.5218 (t70) REVERT: E 310 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7113 (tt) REVERT: E 311 PRO cc_start: 0.7205 (Cg_endo) cc_final: 0.6889 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7754 (ptm-80) cc_final: 0.7106 (ptp90) REVERT: E 429 HIS cc_start: 0.7329 (m90) cc_final: 0.6996 (m90) REVERT: E 473 CYS cc_start: 0.8449 (m) cc_final: 0.8059 (m) REVERT: E 535 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8098 (mt) outliers start: 74 outliers final: 29 residues processed: 207 average time/residue: 1.2920 time to fit residues: 289.9938 Evaluate side-chains 185 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 535 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 189 HIS E 201 HIS E 286 GLN E 320 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.180438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123860 restraints weight = 12164.646| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.33 r_work: 0.3183 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12443 Z= 0.192 Angle : 0.513 7.509 16871 Z= 0.265 Chirality : 0.044 0.249 1850 Planarity : 0.003 0.035 2170 Dihedral : 8.841 89.111 1737 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 5.81 % Allowed : 25.74 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.21), residues: 1512 helix: 1.32 (0.23), residues: 507 sheet: 0.57 (0.28), residues: 356 loop : -1.13 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 PHE 0.011 0.001 PHE E 437 TYR 0.016 0.001 TYR B 135 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 149 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7473 (t0) cc_final: 0.7014 (m-30) REVERT: A 75 LYS cc_start: 0.7656 (ttpp) cc_final: 0.7354 (mtpp) REVERT: A 90 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7026 (mtmp) REVERT: A 290 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7363 (mtpp) REVERT: B 38 LYS cc_start: 0.8773 (ttpp) cc_final: 0.7566 (tptt) REVERT: B 50 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6738 (mp) REVERT: B 51 MET cc_start: 0.7050 (mtp) cc_final: 0.6606 (mtt) REVERT: B 87 ARG cc_start: 0.7238 (ttm170) cc_final: 0.6189 (tmt170) REVERT: B 133 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: B 223 GLU cc_start: 0.6735 (tp30) cc_final: 0.6376 (tp30) REVERT: B 255 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: B 275 CYS cc_start: 0.7539 (m) cc_final: 0.6842 (t) REVERT: B 335 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7181 (p0) REVERT: B 404 GLU cc_start: 0.7889 (tp30) cc_final: 0.7354 (tt0) REVERT: B 440 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7108 (ptm-80) REVERT: B 528 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6665 (mp) REVERT: B 530 ASN cc_start: 0.7571 (m-40) cc_final: 0.7148 (t0) REVERT: D 75 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: E 48 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: E 51 MET cc_start: 0.6884 (mtp) cc_final: 0.6437 (mtt) REVERT: E 101 VAL cc_start: 0.7666 (t) cc_final: 0.7343 (p) REVERT: E 190 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6379 (tt) REVERT: E 192 GLN cc_start: 0.6002 (mt0) cc_final: 0.5750 (tt0) REVERT: E 209 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: E 211 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6411 (mp) REVERT: E 212 SER cc_start: 0.7127 (t) cc_final: 0.6791 (p) REVERT: E 284 SER cc_start: 0.6329 (OUTLIER) cc_final: 0.6094 (t) REVERT: E 310 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7050 (tt) REVERT: E 311 PRO cc_start: 0.7207 (Cg_endo) cc_final: 0.6882 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7046 (ptp90) REVERT: E 348 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6555 (t70) REVERT: E 401 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8133 (mt) REVERT: E 404 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8634 (pt0) REVERT: E 429 HIS cc_start: 0.7354 (m90) cc_final: 0.6996 (m90) REVERT: E 473 CYS cc_start: 0.8476 (m) cc_final: 0.7975 (m) REVERT: E 535 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8172 (mt) outliers start: 77 outliers final: 32 residues processed: 210 average time/residue: 1.2766 time to fit residues: 291.1320 Evaluate side-chains 193 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 535 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 124 optimal weight: 0.0470 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 286 GLN E 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128510 restraints weight = 12225.729| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.47 r_work: 0.3165 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12443 Z= 0.275 Angle : 0.563 7.974 16871 Z= 0.288 Chirality : 0.045 0.275 1850 Planarity : 0.004 0.035 2170 Dihedral : 8.951 89.705 1734 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 6.57 % Allowed : 24.83 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.01 (0.21), residues: 1512 helix: 1.10 (0.23), residues: 513 sheet: 0.49 (0.28), residues: 356 loop : -1.21 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 PHE 0.013 0.001 PHE E 437 TYR 0.018 0.002 TYR B 135 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 136 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7354 (t0) cc_final: 0.7003 (m-30) REVERT: A 90 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7088 (mtmp) REVERT: A 290 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7440 (mtpp) REVERT: B 38 LYS cc_start: 0.8729 (ttpp) cc_final: 0.7527 (tptt) REVERT: B 50 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 87 ARG cc_start: 0.7162 (ttm170) cc_final: 0.6236 (tmt170) REVERT: B 133 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: B 209 ASP cc_start: 0.6442 (m-30) cc_final: 0.6231 (m-30) REVERT: B 223 GLU cc_start: 0.6757 (tp30) cc_final: 0.6406 (tp30) REVERT: B 255 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: B 275 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6906 (t) REVERT: B 335 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7266 (p0) REVERT: B 401 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8395 (mt) REVERT: B 404 GLU cc_start: 0.7706 (tp30) cc_final: 0.7374 (tt0) REVERT: B 440 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6367 (mmm160) REVERT: B 528 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6610 (mp) REVERT: B 530 ASN cc_start: 0.7652 (m-40) cc_final: 0.7241 (t0) REVERT: D 75 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: E 48 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: E 51 MET cc_start: 0.6943 (mtp) cc_final: 0.6519 (mtt) REVERT: E 71 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: E 101 VAL cc_start: 0.7725 (t) cc_final: 0.7402 (p) REVERT: E 190 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6415 (tt) REVERT: E 192 GLN cc_start: 0.6040 (mt0) cc_final: 0.5816 (tt0) REVERT: E 211 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6503 (mp) REVERT: E 212 SER cc_start: 0.7236 (t) cc_final: 0.6925 (p) REVERT: E 213 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5006 (t0) REVERT: E 272 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (p) REVERT: E 284 SER cc_start: 0.6374 (OUTLIER) cc_final: 0.6067 (t) REVERT: E 310 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7093 (tt) REVERT: E 311 PRO cc_start: 0.7178 (Cg_endo) cc_final: 0.6845 (Cg_exo) REVERT: E 348 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6537 (t70) REVERT: E 401 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8083 (mt) REVERT: E 404 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: E 429 HIS cc_start: 0.7361 (m90) cc_final: 0.7041 (m90) REVERT: E 473 CYS cc_start: 0.8494 (m) cc_final: 0.8051 (m) outliers start: 87 outliers final: 38 residues processed: 200 average time/residue: 1.3041 time to fit residues: 283.2428 Evaluate side-chains 196 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 194 GLN B 230 ASN B 292 GLN B 339 HIS E 184 HIS E 201 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.176327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119621 restraints weight = 12398.269| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.35 r_work: 0.3144 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12443 Z= 0.422 Angle : 0.664 9.265 16871 Z= 0.335 Chirality : 0.049 0.305 1850 Planarity : 0.004 0.041 2170 Dihedral : 9.322 90.719 1734 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.24 % Rotamer: Outliers : 6.42 % Allowed : 24.98 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.37 (0.21), residues: 1512 helix: 0.78 (0.23), residues: 502 sheet: 0.27 (0.28), residues: 341 loop : -1.30 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.017 0.002 PHE E 437 TYR 0.019 0.002 TYR B 135 ARG 0.005 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 136 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8450 (tpt) cc_final: 0.8130 (tpp) REVERT: A 63 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: A 71 ASP cc_start: 0.7453 (t0) cc_final: 0.6976 (m-30) REVERT: A 90 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6971 (mtmp) REVERT: A 163 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: A 290 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7381 (mtpp) REVERT: B 38 LYS cc_start: 0.8765 (ttpp) cc_final: 0.7515 (tptt) REVERT: B 50 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6710 (mp) REVERT: B 87 ARG cc_start: 0.7233 (ttm170) cc_final: 0.6185 (tmt170) REVERT: B 133 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: B 209 ASP cc_start: 0.6413 (m-30) cc_final: 0.6201 (m-30) REVERT: B 223 GLU cc_start: 0.6776 (tp30) cc_final: 0.6435 (tp30) REVERT: B 275 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6902 (t) REVERT: B 335 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7572 (p0) REVERT: B 401 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 404 GLU cc_start: 0.7868 (tp30) cc_final: 0.7479 (tt0) REVERT: B 440 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6389 (mmm160) REVERT: B 528 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6706 (mp) REVERT: B 530 ASN cc_start: 0.7637 (m-40) cc_final: 0.7158 (t0) REVERT: D 75 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: E 48 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: E 51 MET cc_start: 0.6972 (mtp) cc_final: 0.6476 (mtt) REVERT: E 190 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6395 (tt) REVERT: E 192 GLN cc_start: 0.6155 (mt0) cc_final: 0.5913 (tt0) REVERT: E 211 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6461 (mp) REVERT: E 212 SER cc_start: 0.7338 (OUTLIER) cc_final: 0.7020 (p) REVERT: E 272 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7340 (p) REVERT: E 284 SER cc_start: 0.6303 (OUTLIER) cc_final: 0.6000 (t) REVERT: E 310 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7103 (tt) REVERT: E 311 PRO cc_start: 0.7174 (Cg_endo) cc_final: 0.6890 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7726 (ptm-80) cc_final: 0.7035 (mtp-110) REVERT: E 348 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6514 (t70) REVERT: E 401 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8108 (mt) REVERT: E 429 HIS cc_start: 0.7366 (m90) cc_final: 0.7001 (m90) REVERT: E 473 CYS cc_start: 0.8484 (m) cc_final: 0.7944 (m) outliers start: 85 outliers final: 39 residues processed: 197 average time/residue: 1.3225 time to fit residues: 282.1954 Evaluate side-chains 192 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 107 optimal weight: 0.0000 chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 220 ASN E 381 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.180719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130172 restraints weight = 12242.107| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.46 r_work: 0.3195 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12443 Z= 0.155 Angle : 0.501 7.484 16871 Z= 0.260 Chirality : 0.043 0.231 1850 Planarity : 0.003 0.036 2170 Dihedral : 8.891 89.692 1734 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 4.83 % Allowed : 26.72 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.02 (0.21), residues: 1512 helix: 1.27 (0.23), residues: 500 sheet: 0.34 (0.28), residues: 350 loop : -1.16 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 PHE 0.011 0.001 PHE E 85 TYR 0.015 0.001 TYR B 135 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7415 (t0) cc_final: 0.7049 (m-30) REVERT: A 75 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7367 (mtpp) REVERT: A 90 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7021 (mtmp) REVERT: B 38 LYS cc_start: 0.8731 (ttpp) cc_final: 0.7558 (tptt) REVERT: B 51 MET cc_start: 0.7179 (mtp) cc_final: 0.6714 (mtt) REVERT: B 87 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6279 (tmt170) REVERT: B 100 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.3374 (mmm160) REVERT: B 133 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: B 223 GLU cc_start: 0.6714 (tp30) cc_final: 0.6379 (tp30) REVERT: B 275 CYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6944 (t) REVERT: B 335 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7084 (p0) REVERT: B 401 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 404 GLU cc_start: 0.7688 (tp30) cc_final: 0.7370 (tt0) REVERT: B 440 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7147 (ptm-80) REVERT: B 528 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6606 (mp) REVERT: B 530 ASN cc_start: 0.7706 (m-40) cc_final: 0.7290 (t0) REVERT: E 51 MET cc_start: 0.6841 (mtp) cc_final: 0.6460 (mtt) REVERT: E 52 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6046 (mttt) REVERT: E 101 VAL cc_start: 0.7667 (t) cc_final: 0.7375 (p) REVERT: E 192 GLN cc_start: 0.6105 (mt0) cc_final: 0.5847 (tt0) REVERT: E 211 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6531 (mp) REVERT: E 212 SER cc_start: 0.7259 (t) cc_final: 0.7002 (p) REVERT: E 213 ASP cc_start: 0.5629 (OUTLIER) cc_final: 0.5317 (t70) REVERT: E 272 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7539 (p) REVERT: E 284 SER cc_start: 0.6338 (OUTLIER) cc_final: 0.6089 (t) REVERT: E 310 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7066 (tt) REVERT: E 311 PRO cc_start: 0.7103 (Cg_endo) cc_final: 0.6785 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7725 (ptm-80) cc_final: 0.7227 (mtp-110) REVERT: E 401 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8125 (mt) REVERT: E 429 HIS cc_start: 0.7345 (m90) cc_final: 0.7022 (m90) REVERT: E 473 CYS cc_start: 0.8419 (m) cc_final: 0.7913 (m) REVERT: E 535 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8084 (mt) outliers start: 64 outliers final: 28 residues processed: 194 average time/residue: 1.3178 time to fit residues: 277.4262 Evaluate side-chains 182 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 535 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 91 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130761 restraints weight = 12242.959| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.27 r_work: 0.3190 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12443 Z= 0.408 Angle : 0.655 8.853 16871 Z= 0.331 Chirality : 0.049 0.298 1850 Planarity : 0.004 0.043 2170 Dihedral : 9.114 90.518 1727 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.76 % Favored : 95.17 % Rotamer: Outliers : 5.06 % Allowed : 25.96 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.37 (0.21), residues: 1512 helix: 0.83 (0.23), residues: 502 sheet: 0.16 (0.28), residues: 345 loop : -1.28 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.016 0.002 PHE E 437 TYR 0.019 0.002 TYR B 135 ARG 0.005 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 136 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7448 (t0) cc_final: 0.7096 (m-30) REVERT: A 99 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7378 (mp0) REVERT: B 38 LYS cc_start: 0.8779 (ttpp) cc_final: 0.7641 (tptt) REVERT: B 51 MET cc_start: 0.7246 (mtp) cc_final: 0.6806 (mtt) REVERT: B 87 ARG cc_start: 0.7302 (ttm170) cc_final: 0.6449 (tmt170) REVERT: B 100 ARG cc_start: 0.4651 (OUTLIER) cc_final: 0.3408 (mmm160) REVERT: B 133 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 209 ASP cc_start: 0.6524 (m-30) cc_final: 0.6308 (m-30) REVERT: B 275 CYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7180 (t) REVERT: B 335 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7531 (p0) REVERT: B 401 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 404 GLU cc_start: 0.7795 (tp30) cc_final: 0.7475 (tt0) REVERT: B 528 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6729 (mp) REVERT: B 530 ASN cc_start: 0.7753 (m-40) cc_final: 0.7347 (t0) REVERT: D 75 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: E 48 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: E 51 MET cc_start: 0.7099 (mtp) cc_final: 0.6667 (mtt) REVERT: E 52 LYS cc_start: 0.7261 (mtpp) cc_final: 0.6368 (mttt) REVERT: E 211 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6706 (mp) REVERT: E 212 SER cc_start: 0.7505 (t) cc_final: 0.7204 (p) REVERT: E 213 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.5385 (t70) REVERT: E 272 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7522 (p) REVERT: E 284 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.6125 (t) REVERT: E 310 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7115 (tt) REVERT: E 311 PRO cc_start: 0.7170 (Cg_endo) cc_final: 0.6845 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7824 (ptm-80) cc_final: 0.7307 (mtp-110) REVERT: E 401 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8250 (mt) REVERT: E 429 HIS cc_start: 0.7391 (m90) cc_final: 0.7124 (m90) REVERT: E 473 CYS cc_start: 0.8501 (m) cc_final: 0.7991 (m) outliers start: 67 outliers final: 35 residues processed: 189 average time/residue: 1.3471 time to fit residues: 277.2912 Evaluate side-chains 183 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134337 restraints weight = 12089.702| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.18 r_work: 0.3250 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12443 Z= 0.165 Angle : 0.508 7.516 16871 Z= 0.264 Chirality : 0.043 0.230 1850 Planarity : 0.004 0.044 2170 Dihedral : 8.711 89.697 1727 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 3.92 % Allowed : 27.32 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.00 (0.21), residues: 1512 helix: 1.28 (0.23), residues: 501 sheet: 0.29 (0.28), residues: 350 loop : -1.16 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.010 0.001 PHE E 85 TYR 0.016 0.001 TYR A 304 ARG 0.007 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7461 (t0) cc_final: 0.7120 (m-30) REVERT: A 75 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7551 (mtpp) REVERT: B 38 LYS cc_start: 0.8804 (ttpp) cc_final: 0.7702 (tptt) REVERT: B 51 MET cc_start: 0.7319 (mtp) cc_final: 0.6875 (mtt) REVERT: B 87 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6472 (tmt170) REVERT: B 133 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: B 275 CYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7074 (t) REVERT: B 335 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7228 (p0) REVERT: B 404 GLU cc_start: 0.7786 (tp30) cc_final: 0.7489 (tt0) REVERT: B 528 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6736 (mp) REVERT: B 530 ASN cc_start: 0.7789 (m-40) cc_final: 0.7410 (t0) REVERT: E 51 MET cc_start: 0.6982 (mtp) cc_final: 0.6621 (mtt) REVERT: E 52 LYS cc_start: 0.7107 (mtpp) cc_final: 0.6218 (mttt) REVERT: E 101 VAL cc_start: 0.7736 (t) cc_final: 0.7454 (p) REVERT: E 211 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6694 (mp) REVERT: E 212 SER cc_start: 0.7402 (t) cc_final: 0.7138 (p) REVERT: E 213 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5363 (t70) REVERT: E 310 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7090 (tt) REVERT: E 311 PRO cc_start: 0.7137 (Cg_endo) cc_final: 0.6820 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7713 (ptm-80) cc_final: 0.7372 (mtp-110) REVERT: E 348 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6528 (t70) REVERT: E 381 GLN cc_start: 0.7372 (mt0) cc_final: 0.7162 (mt0) REVERT: E 401 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8262 (mt) REVERT: E 429 HIS cc_start: 0.7372 (m90) cc_final: 0.7117 (m90) outliers start: 52 outliers final: 31 residues processed: 183 average time/residue: 1.3307 time to fit residues: 263.7400 Evaluate side-chains 179 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 86 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 230 ASN B 292 GLN E 184 HIS E 201 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.183739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131007 restraints weight = 12114.528| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.32 r_work: 0.3293 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12443 Z= 0.181 Angle : 0.517 7.589 16871 Z= 0.268 Chirality : 0.043 0.239 1850 Planarity : 0.004 0.045 2170 Dihedral : 8.565 88.712 1727 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 3.32 % Allowed : 27.70 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.10 (0.21), residues: 1512 helix: 1.41 (0.23), residues: 501 sheet: 0.33 (0.28), residues: 350 loop : -1.13 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.011 0.001 PHE E 437 TYR 0.017 0.001 TYR B 135 ARG 0.008 0.000 ARG B 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.7993 (tpt170) REVERT: A 71 ASP cc_start: 0.7535 (t0) cc_final: 0.7109 (m-30) REVERT: A 75 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7522 (mtpp) REVERT: A 219 LYS cc_start: 0.7323 (tttt) cc_final: 0.7106 (tttt) REVERT: B 38 LYS cc_start: 0.8813 (ttpp) cc_final: 0.7673 (tptt) REVERT: B 50 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.6951 (mp) REVERT: B 51 MET cc_start: 0.7286 (mtp) cc_final: 0.6812 (mtt) REVERT: B 87 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6404 (tmt170) REVERT: B 275 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6907 (t) REVERT: B 335 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7288 (p0) REVERT: B 348 ASP cc_start: 0.8019 (t70) cc_final: 0.7792 (t70) REVERT: B 404 GLU cc_start: 0.7909 (tp30) cc_final: 0.7566 (tt0) REVERT: B 528 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6707 (mp) REVERT: B 530 ASN cc_start: 0.7674 (m-40) cc_final: 0.7290 (t0) REVERT: D 75 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: E 51 MET cc_start: 0.6948 (mtp) cc_final: 0.6551 (mtt) REVERT: E 52 LYS cc_start: 0.6984 (mtpp) cc_final: 0.6077 (mttt) REVERT: E 211 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6565 (mp) REVERT: E 212 SER cc_start: 0.7381 (t) cc_final: 0.7108 (p) REVERT: E 213 ASP cc_start: 0.5688 (OUTLIER) cc_final: 0.5365 (t70) REVERT: E 272 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7595 (p) REVERT: E 310 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7062 (tt) REVERT: E 311 PRO cc_start: 0.7076 (Cg_endo) cc_final: 0.6753 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7627 (ptm-80) cc_final: 0.7301 (mtp-110) REVERT: E 401 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8267 (mt) REVERT: E 429 HIS cc_start: 0.7327 (m90) cc_final: 0.7049 (m90) REVERT: E 535 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8289 (mt) outliers start: 44 outliers final: 29 residues processed: 176 average time/residue: 1.3237 time to fit residues: 252.5030 Evaluate side-chains 178 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 535 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 230 ASN B 255 HIS B 292 GLN E 184 HIS E 201 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.181379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129997 restraints weight = 12073.400| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.36 r_work: 0.3230 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12443 Z= 0.305 Angle : 0.599 8.152 16871 Z= 0.306 Chirality : 0.047 0.280 1850 Planarity : 0.004 0.050 2170 Dihedral : 8.704 90.060 1724 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 3.92 % Allowed : 27.62 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.12 (0.21), residues: 1512 helix: 1.14 (0.23), residues: 501 sheet: 0.26 (0.28), residues: 350 loop : -1.21 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.014 0.001 PHE E 437 TYR 0.018 0.002 TYR B 135 ARG 0.009 0.000 ARG B 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9129.18 seconds wall clock time: 161 minutes 57.75 seconds (9717.75 seconds total)