Starting phenix.real_space_refine on Tue Jun 10 23:50:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtq_47156/06_2025/9dtq_47156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtq_47156/06_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_47156/06_2025/9dtq_47156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtq_47156/06_2025/9dtq_47156.map" model { file = "/net/cci-nas-00/data/ceres_data/9dtq_47156/06_2025/9dtq_47156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtq_47156/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.62, per 1000 atoms: 0.71 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 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: 1.75 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: 4.76 Time building geometry restraints manager: 3.76 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: 53.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.460 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:15.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.720 ------------------------------------------------------------------------------- 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 12445 Z= 0.150 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 Details of bonding type rmsd hydrogen bonds : bond 0.18429 ( 520) hydrogen bonds : angle 6.92627 ( 1440) covalent geometry : bond 0.00320 (12443) covalent geometry : angle 0.54499 (16871) Misc. bond : bond 0.00122 ( 2) *********************** 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 : 1.723 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: 1.4258 time to fit residues: 287.5899 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 : 1.274 ------------------------------------------------------------------------------- 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 = 0.179473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122828 restraints weight = 12171.602| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.34 r_work: 0.3178 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12445 Z= 0.159 Angle : 0.568 8.084 16871 Z= 0.293 Chirality : 0.045 0.272 1850 Planarity : 0.004 0.040 2170 Dihedral : 10.230 90.674 1789 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % 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 E 184 PHE 0.013 0.001 PHE E 437 TYR 0.017 0.002 TYR B 135 ARG 0.003 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 520) hydrogen bonds : angle 5.12689 ( 1440) covalent geometry : bond 0.00381 (12443) covalent geometry : angle 0.56781 (16871) Misc. bond : bond 0.00197 ( 2) *********************** 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 : 1.229 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7437 (t0) cc_final: 0.6962 (m-30) REVERT: A 290 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7370 (mtpp) REVERT: B 38 LYS cc_start: 0.8786 (ttpp) cc_final: 0.7625 (tptt) REVERT: B 50 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6712 (mp) REVERT: B 51 MET cc_start: 0.7117 (mtp) cc_final: 0.6632 (mtt) REVERT: B 87 ARG cc_start: 0.7246 (ttm170) cc_final: 0.6169 (tmt170) REVERT: B 255 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6675 (t-90) REVERT: B 275 CYS cc_start: 0.7458 (m) cc_final: 0.6815 (t) REVERT: B 335 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7055 (p0) REVERT: B 404 GLU cc_start: 0.7854 (tp30) cc_final: 0.7329 (tt0) REVERT: B 505 ASP cc_start: 0.1290 (OUTLIER) cc_final: 0.1081 (m-30) REVERT: B 528 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6519 (mp) REVERT: B 530 ASN cc_start: 0.7619 (m-40) cc_final: 0.7149 (t0) REVERT: E 48 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6547 (mp10) REVERT: E 51 MET cc_start: 0.6888 (mtp) cc_final: 0.6419 (mtt) REVERT: E 174 SER cc_start: 0.7379 (m) cc_final: 0.7122 (t) REVERT: E 190 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6372 (tt) REVERT: E 192 GLN cc_start: 0.5982 (mt0) cc_final: 0.5636 (tt0) REVERT: E 211 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6452 (mp) REVERT: E 212 SER cc_start: 0.7168 (t) cc_final: 0.6815 (p) REVERT: E 310 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7052 (tt) REVERT: E 311 PRO cc_start: 0.7162 (Cg_endo) cc_final: 0.6832 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7778 (ptm-80) cc_final: 0.7084 (ptp90) REVERT: E 401 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8139 (mt) REVERT: E 429 HIS cc_start: 0.7342 (m90) cc_final: 0.6975 (m90) REVERT: E 473 CYS cc_start: 0.8361 (m) cc_final: 0.8151 (m) outliers start: 74 outliers final: 25 residues processed: 208 average time/residue: 1.2572 time to fit residues: 284.9646 Evaluate side-chains 178 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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: 0.9990 chunk 147 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 150 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.180622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130488 restraints weight = 12427.330| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.55 r_work: 0.3184 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12445 Z= 0.123 Angle : 0.514 7.630 16871 Z= 0.266 Chirality : 0.044 0.250 1850 Planarity : 0.003 0.036 2170 Dihedral : 9.104 89.588 1742 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 5.21 % Allowed : 26.34 % 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 (0.22), residues: 1512 helix: 1.27 (0.24), residues: 504 sheet: 0.62 (0.28), residues: 356 loop : -1.11 (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 0.011 0.001 PHE E 437 TYR 0.016 0.001 TYR A 304 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 520) hydrogen bonds : angle 4.80919 ( 1440) covalent geometry : bond 0.00289 (12443) covalent geometry : angle 0.51392 (16871) Misc. bond : bond 0.00136 ( 2) *********************** 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 218 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7339 (t0) cc_final: 0.6999 (m-30) REVERT: A 75 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7375 (mtpp) REVERT: A 290 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7433 (mtpp) REVERT: B 38 LYS cc_start: 0.8732 (ttpp) cc_final: 0.7556 (tptt) REVERT: B 50 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 51 MET cc_start: 0.7091 (mtp) cc_final: 0.6655 (mtt) REVERT: B 87 ARG cc_start: 0.7206 (ttm170) cc_final: 0.6275 (tmt170) REVERT: B 255 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6666 (t70) REVERT: B 275 CYS cc_start: 0.7495 (m) cc_final: 0.6926 (t) REVERT: B 335 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7064 (p0) REVERT: B 404 GLU cc_start: 0.7708 (tp30) cc_final: 0.7410 (tt0) REVERT: B 440 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7124 (ptm-80) REVERT: B 505 ASP cc_start: 0.1520 (OUTLIER) cc_final: 0.1311 (m-30) REVERT: B 528 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6517 (mp) REVERT: B 530 ASN cc_start: 0.7676 (m-40) cc_final: 0.7253 (t0) REVERT: E 51 MET cc_start: 0.6893 (mtp) cc_final: 0.6482 (mtt) REVERT: E 190 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6419 (tt) REVERT: E 192 GLN cc_start: 0.6033 (mt0) cc_final: 0.5671 (tt0) REVERT: E 209 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6093 (m-30) REVERT: E 211 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6458 (mp) REVERT: E 212 SER cc_start: 0.7124 (t) cc_final: 0.6793 (p) REVERT: E 310 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7117 (tt) REVERT: E 311 PRO cc_start: 0.7214 (Cg_endo) cc_final: 0.6885 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7128 (ptp90) REVERT: E 429 HIS cc_start: 0.7333 (m90) cc_final: 0.7008 (m90) REVERT: E 473 CYS cc_start: 0.8440 (m) cc_final: 0.8087 (m) outliers start: 69 outliers final: 25 residues processed: 200 average time/residue: 1.2682 time to fit residues: 275.2866 Evaluate side-chains 176 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU 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 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 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.0040 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.181199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124738 restraints weight = 12136.278| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.32 r_work: 0.3209 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12445 Z= 0.113 Angle : 0.498 7.521 16871 Z= 0.258 Chirality : 0.043 0.241 1850 Planarity : 0.003 0.035 2170 Dihedral : 8.749 88.471 1737 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 5.51 % Allowed : 26.11 % Favored : 68.38 % 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: 0.24 (0.22), residues: 1512 helix: 1.40 (0.23), residues: 507 sheet: 0.58 (0.28), residues: 356 loop : -1.09 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 168 HIS 0.006 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 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 520) hydrogen bonds : angle 4.62198 ( 1440) covalent geometry : bond 0.00264 (12443) covalent geometry : angle 0.49775 (16871) Misc. bond : bond 0.00124 ( 2) *********************** 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 225 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 152 time to evaluate : 1.924 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7461 (t0) cc_final: 0.6998 (m-30) REVERT: A 75 LYS cc_start: 0.7620 (ttpp) cc_final: 0.7328 (mtpp) REVERT: A 90 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7018 (mtmp) REVERT: A 253 TYR cc_start: 0.8785 (t80) cc_final: 0.8583 (t80) REVERT: A 290 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7364 (mtpp) REVERT: B 38 LYS cc_start: 0.8765 (ttpp) cc_final: 0.7555 (tptt) REVERT: B 50 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6762 (mp) REVERT: B 51 MET cc_start: 0.7038 (mtp) cc_final: 0.6600 (mtt) REVERT: B 87 ARG cc_start: 0.7276 (ttm170) cc_final: 0.6236 (tmt170) REVERT: B 255 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6803 (t-90) REVERT: B 275 CYS cc_start: 0.7450 (m) cc_final: 0.6741 (t) REVERT: B 335 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7032 (p0) REVERT: B 368 TYR cc_start: 0.8961 (p90) cc_final: 0.8671 (p90) REVERT: B 404 GLU cc_start: 0.7914 (tp30) cc_final: 0.7377 (tt0) REVERT: B 440 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7100 (ptm-80) REVERT: B 528 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6618 (mp) REVERT: B 530 ASN cc_start: 0.7621 (m-40) cc_final: 0.7172 (t0) REVERT: D 8 GLN cc_start: 0.8341 (mp10) cc_final: 0.8107 (mp-120) REVERT: D 75 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: E 48 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: E 51 MET cc_start: 0.6881 (mtp) cc_final: 0.6429 (mtt) REVERT: E 71 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: E 101 VAL cc_start: 0.7677 (t) cc_final: 0.7347 (p) REVERT: E 192 GLN cc_start: 0.6040 (mt0) cc_final: 0.5675 (tt0) REVERT: E 209 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: E 211 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6437 (mp) REVERT: E 212 SER cc_start: 0.7134 (t) cc_final: 0.6814 (p) REVERT: E 213 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.5185 (t70) REVERT: E 310 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7080 (OUTLIER) REVERT: E 311 PRO cc_start: 0.7205 (Cg_endo) cc_final: 0.6875 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.7065 (mtp-110) REVERT: E 401 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8160 (mt) REVERT: E 429 HIS cc_start: 0.7334 (m90) cc_final: 0.6989 (m90) REVERT: E 473 CYS cc_start: 0.8461 (m) cc_final: 0.7960 (m) outliers start: 73 outliers final: 29 residues processed: 211 average time/residue: 1.4440 time to fit residues: 333.1690 Evaluate side-chains 186 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 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 71 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP 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 258 LEU 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 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 496 VAL 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: 0.0270 chunk 3 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 124 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.179447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128941 restraints weight = 12213.859| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.57 r_work: 0.3171 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12445 Z= 0.151 Angle : 0.545 7.632 16871 Z= 0.279 Chirality : 0.045 0.272 1850 Planarity : 0.003 0.035 2170 Dihedral : 8.801 89.432 1732 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 5.96 % Allowed : 25.13 % Favored : 68.91 % 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: 0.07 (0.21), residues: 1512 helix: 1.27 (0.23), residues: 507 sheet: 0.44 (0.28), residues: 350 loop : -1.15 (0.23), residues: 655 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 0.004 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 520) hydrogen bonds : angle 4.69053 ( 1440) covalent geometry : bond 0.00369 (12443) covalent geometry : angle 0.54498 (16871) Misc. bond : bond 0.00183 ( 2) *********************** 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 215 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 136 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7363 (t0) cc_final: 0.7007 (m-30) REVERT: A 75 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7447 (mtpp) REVERT: A 90 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7068 (mtmp) REVERT: A 290 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7453 (mtpp) REVERT: A 298 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8341 (mtm) REVERT: B 38 LYS cc_start: 0.8733 (ttpp) cc_final: 0.7552 (tptt) REVERT: B 50 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6810 (mp) REVERT: B 51 MET cc_start: 0.7083 (mtp) cc_final: 0.6621 (mtt) REVERT: B 87 ARG cc_start: 0.7188 (ttm170) cc_final: 0.6244 (tmt170) REVERT: B 209 ASP cc_start: 0.6441 (m-30) cc_final: 0.6208 (m-30) REVERT: B 223 GLU cc_start: 0.6724 (tp30) cc_final: 0.6383 (tp30) REVERT: B 255 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6903 (t-90) REVERT: B 275 CYS cc_start: 0.7387 (m) cc_final: 0.6878 (t) REVERT: B 335 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7229 (p0) REVERT: B 401 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 404 GLU cc_start: 0.7721 (tp30) cc_final: 0.7385 (tt0) REVERT: B 528 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6570 (mp) REVERT: B 530 ASN cc_start: 0.7622 (m-40) cc_final: 0.7228 (t0) REVERT: D 75 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: E 48 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: E 51 MET cc_start: 0.6939 (mtp) cc_final: 0.6511 (mtt) REVERT: E 101 VAL cc_start: 0.7724 (t) cc_final: 0.7401 (p) REVERT: E 192 GLN cc_start: 0.6048 (mt0) cc_final: 0.5819 (tt0) REVERT: E 209 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6170 (m-30) REVERT: E 211 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6439 (mp) REVERT: E 212 SER cc_start: 0.7144 (t) cc_final: 0.6829 (p) REVERT: E 213 ASP cc_start: 0.5620 (OUTLIER) cc_final: 0.5228 (t70) REVERT: E 284 SER cc_start: 0.6330 (OUTLIER) cc_final: 0.6085 (t) REVERT: E 310 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7096 (tt) REVERT: E 311 PRO cc_start: 0.7164 (Cg_endo) cc_final: 0.6864 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7787 (ptm-80) cc_final: 0.7167 (mtp-110) REVERT: E 320 ASN cc_start: 0.5135 (OUTLIER) cc_final: 0.4914 (m-40) REVERT: E 348 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6536 (t70) REVERT: E 401 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8085 (mt) REVERT: E 429 HIS cc_start: 0.7363 (m90) cc_final: 0.7052 (m90) REVERT: E 473 CYS cc_start: 0.8473 (m) cc_final: 0.8031 (m) outliers start: 79 outliers final: 37 residues processed: 197 average time/residue: 1.5705 time to fit residues: 336.9652 Evaluate side-chains 190 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 A residue 298 MET 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 106 ASP 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 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 401 LEU Chi-restraints excluded: chain B residue 437 PHE 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 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 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 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 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 320 ASN 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 455 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.178547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121757 restraints weight = 12378.313| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.34 r_work: 0.3161 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12445 Z= 0.182 Angle : 0.575 7.796 16871 Z= 0.293 Chirality : 0.046 0.281 1850 Planarity : 0.004 0.035 2170 Dihedral : 8.941 89.886 1732 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 5.66 % Allowed : 25.58 % 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: -0.11 (0.21), residues: 1512 helix: 1.05 (0.23), residues: 514 sheet: 0.37 (0.28), residues: 350 loop : -1.24 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.004 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 520) hydrogen bonds : angle 4.74201 ( 1440) covalent geometry : bond 0.00451 (12443) covalent geometry : angle 0.57517 (16871) Misc. bond : bond 0.00221 ( 2) *********************** 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 211 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 136 time to evaluate : 1.420 Fit side-chains REVERT: A 71 ASP cc_start: 0.7486 (t0) cc_final: 0.7011 (m-30) REVERT: A 90 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6966 (mtmp) REVERT: A 219 LYS cc_start: 0.7403 (tttt) cc_final: 0.7142 (tttt) REVERT: A 290 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7392 (mtpp) REVERT: A 298 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8513 (mtm) REVERT: B 27 MET cc_start: 0.5182 (OUTLIER) cc_final: 0.4905 (mmt) REVERT: B 38 LYS cc_start: 0.8772 (ttpp) cc_final: 0.7525 (tptt) REVERT: B 50 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6747 (mp) REVERT: B 51 MET cc_start: 0.7110 (mtp) cc_final: 0.6613 (mtt) REVERT: B 87 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6179 (tmt170) REVERT: B 223 GLU cc_start: 0.6719 (tp30) cc_final: 0.6357 (tp30) REVERT: B 255 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7071 (t-90) REVERT: B 275 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6792 (t) REVERT: B 335 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7306 (p0) REVERT: B 401 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 404 GLU cc_start: 0.7882 (tp30) cc_final: 0.7490 (tt0) REVERT: B 440 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6382 (mmm160) REVERT: B 528 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 530 ASN cc_start: 0.7627 (m-40) cc_final: 0.7172 (t0) REVERT: D 75 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: E 48 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6709 (mp10) REVERT: E 51 MET cc_start: 0.6919 (mtp) cc_final: 0.6466 (mtt) REVERT: E 71 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: E 101 VAL cc_start: 0.7701 (t) cc_final: 0.7401 (p) REVERT: E 192 GLN cc_start: 0.6089 (mt0) cc_final: 0.5812 (tt0) REVERT: E 211 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6383 (mp) REVERT: E 212 SER cc_start: 0.7250 (t) cc_final: 0.6990 (p) REVERT: E 213 ASP cc_start: 0.5643 (OUTLIER) cc_final: 0.4972 (t0) REVERT: E 310 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7103 (tt) REVERT: E 311 PRO cc_start: 0.7168 (Cg_endo) cc_final: 0.6873 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7715 (ptm-80) cc_final: 0.7029 (mtp-110) REVERT: E 348 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6470 (t70) REVERT: E 401 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8132 (mt) REVERT: E 429 HIS cc_start: 0.7389 (m90) cc_final: 0.7040 (m90) REVERT: E 473 CYS cc_start: 0.8504 (m) cc_final: 0.7978 (m) REVERT: E 535 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (mt) outliers start: 75 outliers final: 34 residues processed: 191 average time/residue: 1.8317 time to fit residues: 381.1920 Evaluate side-chains 188 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 A residue 298 MET Chi-restraints excluded: chain B residue 27 MET 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 106 ASP 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 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 71 GLU 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 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 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 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 Chi-restraints excluded: chain E residue 535 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.184683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131292 restraints weight = 12171.800| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.60 r_work: 0.3289 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12445 Z= 0.107 Angle : 0.489 7.484 16871 Z= 0.254 Chirality : 0.043 0.231 1850 Planarity : 0.003 0.034 2170 Dihedral : 8.610 88.470 1729 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 4.60 % Allowed : 26.49 % Favored : 68.91 % 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: 0.15 (0.21), residues: 1512 helix: 1.41 (0.23), residues: 507 sheet: 0.44 (0.28), residues: 350 loop : -1.15 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 PHE 0.010 0.001 PHE E 437 TYR 0.015 0.001 TYR B 135 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 520) hydrogen bonds : angle 4.52617 ( 1440) covalent geometry : bond 0.00250 (12443) covalent geometry : angle 0.48868 (16871) Misc. bond : bond 0.00115 ( 2) *********************** 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 205 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7583 (t0) cc_final: 0.7149 (m-30) REVERT: A 75 LYS cc_start: 0.7839 (ttpp) cc_final: 0.7549 (mtpp) REVERT: A 90 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7090 (mtmp) REVERT: A 219 LYS cc_start: 0.7368 (tttt) cc_final: 0.7149 (tttt) REVERT: A 253 TYR cc_start: 0.8849 (t80) cc_final: 0.8625 (t80) REVERT: A 298 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8478 (mtm) REVERT: B 27 MET cc_start: 0.5191 (OUTLIER) cc_final: 0.4900 (mmt) REVERT: B 38 LYS cc_start: 0.8847 (ttpp) cc_final: 0.7713 (tptt) REVERT: B 51 MET cc_start: 0.7214 (mtp) cc_final: 0.6794 (mtt) REVERT: B 87 ARG cc_start: 0.7381 (ttm170) cc_final: 0.6400 (tmt170) REVERT: B 100 ARG cc_start: 0.4432 (OUTLIER) cc_final: 0.3832 (mmm160) REVERT: B 129 GLU cc_start: 0.7601 (mp0) cc_final: 0.7158 (mp0) REVERT: B 223 GLU cc_start: 0.6728 (tp30) cc_final: 0.6374 (tp30) REVERT: B 255 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.7078 (t-90) REVERT: B 275 CYS cc_start: 0.7513 (m) cc_final: 0.6822 (t) REVERT: B 335 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7213 (p0) REVERT: B 404 GLU cc_start: 0.7979 (tp30) cc_final: 0.7674 (tt0) REVERT: B 440 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7267 (ptm-80) REVERT: B 528 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6799 (mp) REVERT: B 530 ASN cc_start: 0.7721 (m-40) cc_final: 0.7336 (t0) REVERT: D 75 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: E 51 MET cc_start: 0.7020 (mtp) cc_final: 0.6620 (mtt) REVERT: E 192 GLN cc_start: 0.6179 (mt0) cc_final: 0.5954 (tt0) REVERT: E 211 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6502 (mp) REVERT: E 212 SER cc_start: 0.7252 (t) cc_final: 0.6950 (p) REVERT: E 213 ASP cc_start: 0.5558 (OUTLIER) cc_final: 0.4935 (t0) REVERT: E 310 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7097 (tt) REVERT: E 311 PRO cc_start: 0.7148 (Cg_endo) cc_final: 0.6837 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7719 (ptm-80) cc_final: 0.7146 (mtp-110) REVERT: E 401 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8294 (mt) REVERT: E 429 HIS cc_start: 0.7357 (m90) cc_final: 0.7064 (m90) REVERT: E 473 CYS cc_start: 0.8489 (m) cc_final: 0.7951 (m) outliers start: 61 outliers final: 28 residues processed: 192 average time/residue: 1.3959 time to fit residues: 290.8737 Evaluate side-chains 179 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 298 MET Chi-restraints excluded: chain B residue 27 MET 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 100 ARG Chi-restraints excluded: chain B residue 106 ASP 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 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 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 460 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR 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: 0.8980 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.182530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129146 restraints weight = 12252.094| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.34 r_work: 0.3255 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12445 Z= 0.157 Angle : 0.548 7.689 16871 Z= 0.281 Chirality : 0.045 0.270 1850 Planarity : 0.004 0.034 2170 Dihedral : 8.717 89.379 1726 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 4.68 % Allowed : 26.72 % 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: 0.04 (0.21), residues: 1512 helix: 1.28 (0.23), residues: 501 sheet: 0.38 (0.28), residues: 350 loop : -1.15 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.004 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 520) hydrogen bonds : angle 4.63119 ( 1440) covalent geometry : bond 0.00384 (12443) covalent geometry : angle 0.54846 (16871) Misc. bond : bond 0.00194 ( 2) *********************** 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 201 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7557 (t0) cc_final: 0.7126 (m-30) REVERT: A 90 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7089 (mtmp) REVERT: A 298 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: B 27 MET cc_start: 0.5252 (OUTLIER) cc_final: 0.4945 (mmt) REVERT: B 38 LYS cc_start: 0.8832 (ttpp) cc_final: 0.7689 (tptt) REVERT: B 50 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.6992 (mp) REVERT: B 51 MET cc_start: 0.7227 (mtp) cc_final: 0.6762 (mtt) REVERT: B 87 ARG cc_start: 0.7372 (ttm170) cc_final: 0.6414 (tmt170) REVERT: B 100 ARG cc_start: 0.4316 (OUTLIER) cc_final: 0.3517 (mmm160) REVERT: B 223 GLU cc_start: 0.6742 (tp30) cc_final: 0.6425 (tp30) REVERT: B 255 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.7089 (t-90) REVERT: B 275 CYS cc_start: 0.7633 (m) cc_final: 0.6951 (t) REVERT: B 335 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 401 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8485 (mt) REVERT: B 404 GLU cc_start: 0.7957 (tp30) cc_final: 0.7637 (tt0) REVERT: B 440 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6444 (mmm160) REVERT: B 528 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6811 (mp) REVERT: B 530 ASN cc_start: 0.7733 (m-40) cc_final: 0.7318 (t0) REVERT: D 75 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: E 51 MET cc_start: 0.7033 (mtp) cc_final: 0.6658 (mtt) REVERT: E 101 VAL cc_start: 0.7749 (t) cc_final: 0.7435 (p) REVERT: E 192 GLN cc_start: 0.6168 (mt0) cc_final: 0.5912 (tt0) REVERT: E 211 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6443 (mp) REVERT: E 212 SER cc_start: 0.7302 (t) cc_final: 0.6985 (p) REVERT: E 213 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5052 (t0) REVERT: E 310 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7094 (tt) REVERT: E 311 PRO cc_start: 0.7139 (Cg_endo) cc_final: 0.6846 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7127 (mtp-110) REVERT: E 401 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8244 (mt) REVERT: E 429 HIS cc_start: 0.7392 (m90) cc_final: 0.7094 (m90) REVERT: E 473 CYS cc_start: 0.8485 (m) cc_final: 0.7947 (m) outliers start: 62 outliers final: 33 residues processed: 187 average time/residue: 1.5030 time to fit residues: 302.9893 Evaluate side-chains 184 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 262 CYS Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 27 MET 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 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 163 CYS 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 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 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 102 ILE 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 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: 1.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN 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 = 0.4031 r_free = 0.4031 target = 0.182833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129707 restraints weight = 12117.752| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.36 r_work: 0.3281 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12445 Z= 0.143 Angle : 0.535 7.622 16871 Z= 0.275 Chirality : 0.045 0.258 1850 Planarity : 0.003 0.034 2170 Dihedral : 8.702 89.554 1726 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 4.68 % Allowed : 26.49 % Favored : 68.83 % 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: 0.05 (0.21), residues: 1512 helix: 1.30 (0.23), residues: 501 sheet: 0.36 (0.28), residues: 350 loop : -1.14 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.012 0.001 PHE E 437 TYR 0.017 0.001 TYR B 135 ARG 0.004 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 520) hydrogen bonds : angle 4.62960 ( 1440) covalent geometry : bond 0.00349 (12443) covalent geometry : angle 0.53460 (16871) Misc. bond : bond 0.00175 ( 2) *********************** 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 198 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7523 (t0) cc_final: 0.7101 (m-30) REVERT: A 90 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6995 (mtmp) REVERT: A 298 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: B 27 MET cc_start: 0.5247 (OUTLIER) cc_final: 0.4929 (mmt) REVERT: B 38 LYS cc_start: 0.8808 (ttpp) cc_final: 0.7651 (tptt) REVERT: B 50 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.6946 (mp) REVERT: B 51 MET cc_start: 0.7200 (mtp) cc_final: 0.6740 (mtt) REVERT: B 87 ARG cc_start: 0.7341 (ttm170) cc_final: 0.6370 (tmt170) REVERT: B 100 ARG cc_start: 0.4347 (OUTLIER) cc_final: 0.3544 (mmm160) REVERT: B 275 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6907 (t) REVERT: B 335 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 404 GLU cc_start: 0.7918 (tp30) cc_final: 0.7592 (tt0) REVERT: B 440 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6410 (mmm160) REVERT: B 441 MET cc_start: 0.8826 (ptp) cc_final: 0.8608 (ptp) REVERT: B 528 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6785 (mp) REVERT: B 530 ASN cc_start: 0.7703 (m-40) cc_final: 0.7303 (t0) REVERT: D 75 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: E 51 MET cc_start: 0.6970 (mtp) cc_final: 0.6593 (mtt) REVERT: E 192 GLN cc_start: 0.6126 (mt0) cc_final: 0.5867 (tt0) REVERT: E 209 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6218 (m-30) REVERT: E 211 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6502 (mp) REVERT: E 212 SER cc_start: 0.7310 (t) cc_final: 0.6986 (p) REVERT: E 213 ASP cc_start: 0.5619 (OUTLIER) cc_final: 0.5275 (t70) REVERT: E 310 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7087 (tt) REVERT: E 311 PRO cc_start: 0.7077 (Cg_endo) cc_final: 0.6795 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7698 (ptm-80) cc_final: 0.7114 (mtp-110) REVERT: E 401 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8250 (mt) REVERT: E 429 HIS cc_start: 0.7358 (m90) cc_final: 0.7054 (m90) outliers start: 62 outliers final: 37 residues processed: 185 average time/residue: 1.3088 time to fit residues: 261.7346 Evaluate side-chains 189 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 298 MET Chi-restraints excluded: chain B residue 27 MET 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 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 106 ASP 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 258 LEU 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 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 SER 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 D residue 116 MET Chi-restraints excluded: chain E residue 46 VAL 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 209 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 102 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.184617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134653 restraints weight = 12136.001| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.19 r_work: 0.3245 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12445 Z= 0.108 Angle : 0.500 7.449 16871 Z= 0.260 Chirality : 0.043 0.231 1850 Planarity : 0.003 0.044 2170 Dihedral : 8.494 88.312 1726 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 4.15 % Allowed : 27.62 % Favored : 68.23 % 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: 0.19 (0.21), residues: 1512 helix: 1.46 (0.24), residues: 502 sheet: 0.40 (0.28), residues: 350 loop : -1.09 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 PHE 0.010 0.001 PHE E 437 TYR 0.016 0.001 TYR B 135 ARG 0.008 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 520) hydrogen bonds : angle 4.52684 ( 1440) covalent geometry : bond 0.00251 (12443) covalent geometry : angle 0.49961 (16871) Misc. bond : bond 0.00117 ( 2) ********************** 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 195 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7482 (t0) cc_final: 0.7163 (m-30) REVERT: A 75 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7628 (mtpp) REVERT: A 90 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7215 (mtmp) REVERT: A 298 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8320 (mtm) REVERT: B 38 LYS cc_start: 0.8795 (ttpp) cc_final: 0.7716 (tptt) REVERT: B 50 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7092 (mp) REVERT: B 51 MET cc_start: 0.7240 (mtp) cc_final: 0.6852 (mtt) REVERT: B 87 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6487 (tmt170) REVERT: B 100 ARG cc_start: 0.4419 (OUTLIER) cc_final: 0.3609 (mmm160) REVERT: B 275 CYS cc_start: 0.7542 (m) cc_final: 0.6992 (t) REVERT: B 335 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7092 (p0) REVERT: B 404 GLU cc_start: 0.7819 (tp30) cc_final: 0.7417 (tt0) REVERT: B 440 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7283 (ptm-80) REVERT: B 528 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6728 (mp) REVERT: B 530 ASN cc_start: 0.7707 (m-40) cc_final: 0.7390 (t0) REVERT: D 75 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: E 51 MET cc_start: 0.7026 (mtp) cc_final: 0.6675 (mtt) REVERT: E 101 VAL cc_start: 0.7763 (t) cc_final: 0.7478 (p) REVERT: E 209 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6124 (m-30) REVERT: E 211 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6640 (mp) REVERT: E 212 SER cc_start: 0.7292 (t) cc_final: 0.7024 (p) REVERT: E 213 ASP cc_start: 0.5607 (OUTLIER) cc_final: 0.5318 (t70) REVERT: E 310 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7099 (tt) REVERT: E 311 PRO cc_start: 0.7068 (Cg_endo) cc_final: 0.6773 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7245 (mtp-110) REVERT: E 401 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8301 (mt) REVERT: E 429 HIS cc_start: 0.7345 (m90) cc_final: 0.7082 (m90) outliers start: 55 outliers final: 34 residues processed: 182 average time/residue: 1.3354 time to fit residues: 263.8951 Evaluate side-chains 184 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 262 CYS Chi-restraints excluded: chain A residue 298 MET 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 100 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 163 CYS 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 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 D residue 116 MET Chi-restraints excluded: chain E residue 46 VAL 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 209 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 229 ILE 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.8980 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 255 HIS B 292 GLN D 8 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 = 0.4035 r_free = 0.4035 target = 0.183229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133317 restraints weight = 12057.489| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.18 r_work: 0.3212 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12445 Z= 0.138 Angle : 0.538 7.485 16871 Z= 0.279 Chirality : 0.045 0.255 1850 Planarity : 0.004 0.046 2170 Dihedral : 8.444 88.847 1724 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 4.15 % Allowed : 27.55 % 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: 0.11 (0.21), residues: 1512 helix: 1.39 (0.23), residues: 501 sheet: 0.37 (0.28), residues: 350 loop : -1.13 (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 0.012 0.001 PHE E 437 TYR 0.017 0.001 TYR B 135 ARG 0.008 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 520) hydrogen bonds : angle 4.59534 ( 1440) covalent geometry : bond 0.00334 (12443) covalent geometry : angle 0.53841 (16871) Misc. bond : bond 0.00165 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10552.16 seconds wall clock time: 187 minutes 16.65 seconds (11236.65 seconds total)