Starting phenix.real_space_refine on Wed Sep 17 23:27:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtq_47156/09_2025/9dtq_47156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtq_47156/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dtq_47156/09_2025/9dtq_47156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtq_47156/09_2025/9dtq_47156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dtq_47156/09_2025/9dtq_47156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtq_47156/09_2025/9dtq_47156.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.15, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 595.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.30 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: 1.93 Time building geometry restraints manager: 1.38 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (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 ARG 0.005 0.000 ARG E 87 TYR 0.016 0.001 TYR A 304 PHE 0.011 0.001 PHE E 437 TRP 0.017 0.001 TRP B 168 HIS 0.014 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00320 (12443) covalent geometry : angle 0.54499 (16871) hydrogen bonds : bond 0.18429 ( 520) hydrogen bonds : angle 6.92627 ( 1440) 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 : 0.497 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: 0.6723 time to fit residues: 135.0873 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 : 0.480 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.2980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.178670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122022 restraints weight = 12208.502| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.34 r_work: 0.3166 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12445 Z= 0.180 Angle : 0.594 8.301 16871 Z= 0.304 Chirality : 0.046 0.284 1850 Planarity : 0.004 0.040 2170 Dihedral : 10.311 89.542 1789 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 5.89 % Allowed : 25.13 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.21), residues: 1512 helix: 0.84 (0.23), residues: 511 sheet: 0.58 (0.28), residues: 356 loop : -1.15 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 87 TYR 0.018 0.002 TYR B 135 PHE 0.014 0.002 PHE E 437 TRP 0.009 0.001 TRP D 69 HIS 0.008 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00440 (12443) covalent geometry : angle 0.59351 (16871) hydrogen bonds : bond 0.04717 ( 520) hydrogen bonds : angle 5.13072 ( 1440) Misc. bond : bond 0.00227 ( 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: 78 poor density : 146 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7459 (t0) cc_final: 0.6978 (m-30) REVERT: A 290 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7366 (mtpp) REVERT: B 38 LYS cc_start: 0.8793 (ttpp) cc_final: 0.7637 (tptt) REVERT: B 50 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6702 (mp) REVERT: B 51 MET cc_start: 0.7142 (mtp) cc_final: 0.6649 (mtt) REVERT: B 87 ARG cc_start: 0.7280 (ttm170) cc_final: 0.6206 (tmt170) REVERT: B 255 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6850 (t-90) REVERT: B 275 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6829 (t) REVERT: B 335 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7128 (p0) REVERT: B 404 GLU cc_start: 0.7861 (tp30) cc_final: 0.7334 (tt0) REVERT: B 505 ASP cc_start: 0.1287 (OUTLIER) cc_final: 0.1073 (m-30) REVERT: B 528 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6549 (mp) REVERT: B 530 ASN cc_start: 0.7647 (m-40) cc_final: 0.7160 (t0) REVERT: D 44 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7237 (mmmm) REVERT: E 48 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: E 51 MET cc_start: 0.6936 (mtp) cc_final: 0.6467 (mtt) REVERT: E 174 SER cc_start: 0.7392 (m) cc_final: 0.7136 (t) REVERT: E 190 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6410 (tt) REVERT: E 192 GLN cc_start: 0.5980 (mt0) cc_final: 0.5583 (tt0) REVERT: E 211 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6473 (mp) REVERT: E 212 SER cc_start: 0.7192 (t) cc_final: 0.6841 (p) REVERT: E 310 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7046 (tt) REVERT: E 311 PRO cc_start: 0.7156 (Cg_endo) cc_final: 0.6825 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7774 (ptm-80) cc_final: 0.7077 (ptp90) REVERT: E 401 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8113 (mt) REVERT: E 429 HIS cc_start: 0.7356 (m90) cc_final: 0.6979 (m90) REVERT: E 473 CYS cc_start: 0.8361 (m) cc_final: 0.8153 (m) outliers start: 78 outliers final: 29 residues processed: 208 average time/residue: 0.6300 time to fit residues: 142.0015 Evaluate side-chains 183 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP 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 160 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 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 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 44 LYS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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 = 0.3976 r_free = 0.3976 target = 0.179907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123307 restraints weight = 12301.584| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.33 r_work: 0.3182 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12445 Z= 0.137 Angle : 0.530 7.567 16871 Z= 0.274 Chirality : 0.044 0.256 1850 Planarity : 0.003 0.037 2170 Dihedral : 9.410 90.130 1747 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 5.89 % Allowed : 25.58 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.21), residues: 1512 helix: 1.06 (0.23), residues: 511 sheet: 0.57 (0.28), residues: 356 loop : -1.20 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.017 0.001 TYR A 304 PHE 0.012 0.001 PHE E 437 TRP 0.011 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00327 (12443) covalent geometry : angle 0.53016 (16871) hydrogen bonds : bond 0.04059 ( 520) hydrogen bonds : angle 4.84245 ( 1440) Misc. bond : bond 0.00157 ( 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 227 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 149 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7476 (t0) cc_final: 0.6995 (m-30) REVERT: A 75 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7387 (mtpp) REVERT: A 290 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7372 (mtpp) REVERT: B 38 LYS cc_start: 0.8769 (ttpp) cc_final: 0.7545 (tptt) REVERT: B 50 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6686 (mp) REVERT: B 51 MET cc_start: 0.7086 (mtp) cc_final: 0.6593 (mtt) REVERT: B 87 ARG cc_start: 0.7234 (ttm170) cc_final: 0.6186 (tmt170) REVERT: B 133 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: B 223 GLU cc_start: 0.6713 (tp30) cc_final: 0.6352 (tp30) REVERT: B 255 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6905 (t-90) REVERT: B 275 CYS cc_start: 0.7536 (m) cc_final: 0.6850 (t) REVERT: B 335 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7065 (p0) REVERT: B 404 GLU cc_start: 0.7889 (tp30) cc_final: 0.7506 (tt0) REVERT: B 440 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7110 (ptm-80) REVERT: B 528 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6576 (mp) REVERT: B 530 ASN cc_start: 0.7556 (m-40) cc_final: 0.7125 (t0) REVERT: D 75 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: E 51 MET cc_start: 0.6855 (mtp) cc_final: 0.6408 (mtt) REVERT: E 65 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7859 (mt) REVERT: E 71 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: E 190 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6399 (tt) REVERT: E 192 GLN cc_start: 0.5871 (mt0) cc_final: 0.5551 (tt0) REVERT: E 209 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6135 (m-30) REVERT: E 211 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6480 (mp) REVERT: E 212 SER cc_start: 0.7188 (t) cc_final: 0.6846 (p) REVERT: E 213 ASP cc_start: 0.5656 (OUTLIER) cc_final: 0.5260 (t70) REVERT: E 310 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7064 (tt) REVERT: E 311 PRO cc_start: 0.7188 (Cg_endo) cc_final: 0.6848 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7712 (ptm-80) cc_final: 0.7025 (ptp90) REVERT: E 401 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 429 HIS cc_start: 0.7356 (m90) cc_final: 0.6989 (m90) REVERT: E 473 CYS cc_start: 0.8478 (m) cc_final: 0.8023 (m) outliers start: 78 outliers final: 26 residues processed: 208 average time/residue: 0.6322 time to fit residues: 142.9011 Evaluate side-chains 182 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 133 GLU 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 288 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 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 E residue 46 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 GLU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 93 optimal weight: 0.0870 chunk 91 optimal weight: 6.9990 chunk 130 optimal weight: 0.0070 chunk 128 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 189 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 = 0.3978 r_free = 0.3978 target = 0.180163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123315 restraints weight = 12316.815| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.35 r_work: 0.3181 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12445 Z= 0.129 Angle : 0.522 7.528 16871 Z= 0.270 Chirality : 0.044 0.253 1850 Planarity : 0.003 0.035 2170 Dihedral : 8.928 89.380 1739 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 5.89 % Allowed : 25.13 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.21), residues: 1512 helix: 1.25 (0.23), residues: 507 sheet: 0.56 (0.28), residues: 356 loop : -1.14 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.017 0.001 TYR B 135 PHE 0.012 0.001 PHE E 437 TRP 0.011 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00309 (12443) covalent geometry : angle 0.52198 (16871) hydrogen bonds : bond 0.03814 ( 520) hydrogen bonds : angle 4.68674 ( 1440) Misc. bond : bond 0.00150 ( 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 227 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 149 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7453 (t0) cc_final: 0.6982 (m-30) REVERT: A 75 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7337 (mtpp) REVERT: A 90 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7018 (mtmp) REVERT: A 290 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7347 (mtpp) REVERT: B 38 LYS cc_start: 0.8769 (ttpp) cc_final: 0.7543 (tptt) REVERT: B 50 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6699 (mp) REVERT: B 51 MET cc_start: 0.7025 (mtp) cc_final: 0.6546 (mtt) REVERT: B 87 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6179 (tmt170) REVERT: B 133 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 223 GLU cc_start: 0.6725 (tp30) cc_final: 0.6372 (tp30) REVERT: B 255 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: B 275 CYS cc_start: 0.7432 (m) cc_final: 0.6720 (t) REVERT: B 335 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7103 (p0) REVERT: B 404 GLU cc_start: 0.7866 (tp30) cc_final: 0.7483 (tt0) REVERT: B 440 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7120 (ptm-80) REVERT: B 528 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6633 (mp) REVERT: B 530 ASN cc_start: 0.7585 (m-40) cc_final: 0.7157 (t0) REVERT: D 75 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: E 48 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: E 51 MET cc_start: 0.6877 (mtp) cc_final: 0.6427 (mtt) REVERT: E 101 VAL cc_start: 0.7718 (t) cc_final: 0.7366 (p) REVERT: E 190 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6356 (tt) REVERT: E 192 GLN cc_start: 0.6056 (mt0) cc_final: 0.5781 (tt0) REVERT: E 209 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6184 (m-30) REVERT: E 211 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6423 (mp) REVERT: E 212 SER cc_start: 0.7170 (t) cc_final: 0.6835 (p) REVERT: E 213 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.5239 (t70) REVERT: E 310 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7051 (tt) REVERT: E 311 PRO cc_start: 0.7131 (Cg_endo) cc_final: 0.6827 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7733 (ptm-80) cc_final: 0.7043 (ptp90) REVERT: E 348 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6563 (t70) REVERT: E 429 HIS cc_start: 0.7351 (m90) cc_final: 0.6997 (m90) REVERT: E 473 CYS cc_start: 0.8478 (m) cc_final: 0.7984 (m) REVERT: E 535 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8161 (mt) outliers start: 78 outliers final: 31 residues processed: 208 average time/residue: 0.6229 time to fit residues: 140.8764 Evaluate side-chains 193 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 106 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 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 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 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 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 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 Chi-restraints excluded: chain E residue 535 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.179532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122709 restraints weight = 12282.838| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.34 r_work: 0.3175 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1142 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= 0.146 Angle : 0.538 7.657 16871 Z= 0.277 Chirality : 0.045 0.264 1850 Planarity : 0.004 0.035 2170 Dihedral : 8.885 89.487 1734 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 6.26 % Allowed : 25.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.21), residues: 1512 helix: 1.14 (0.23), residues: 513 sheet: 0.50 (0.28), residues: 356 loop : -1.21 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.017 0.001 TYR B 135 PHE 0.012 0.001 PHE E 437 TRP 0.012 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00357 (12443) covalent geometry : angle 0.53839 (16871) hydrogen bonds : bond 0.03932 ( 520) hydrogen bonds : angle 4.69447 ( 1440) Misc. bond : bond 0.00174 ( 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 222 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 139 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7458 (t0) cc_final: 0.6993 (m-30) REVERT: A 75 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7441 (mtpp) REVERT: A 90 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7007 (mtmp) REVERT: A 290 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7383 (mtpp) REVERT: B 38 LYS cc_start: 0.8768 (ttpp) cc_final: 0.7547 (tptt) REVERT: B 50 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6738 (mp) REVERT: B 51 MET cc_start: 0.7076 (mtp) cc_final: 0.6595 (mtt) REVERT: B 87 ARG cc_start: 0.7233 (ttm170) cc_final: 0.6191 (tmt170) REVERT: B 133 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: B 223 GLU cc_start: 0.6686 (tp30) cc_final: 0.6309 (tp30) REVERT: B 255 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: B 275 CYS cc_start: 0.7483 (m) cc_final: 0.6740 (t) REVERT: B 335 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7219 (p0) REVERT: B 401 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 404 GLU cc_start: 0.7863 (tp30) cc_final: 0.7485 (tt0) REVERT: B 440 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6313 (mmm160) REVERT: B 528 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6669 (mp) REVERT: B 530 ASN cc_start: 0.7627 (m-40) cc_final: 0.7179 (t0) REVERT: D 75 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: E 48 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6733 (mp10) REVERT: E 51 MET cc_start: 0.6904 (mtp) cc_final: 0.6456 (mtt) REVERT: E 190 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6365 (tt) REVERT: E 192 GLN cc_start: 0.6027 (mt0) cc_final: 0.5768 (tt0) REVERT: E 209 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6196 (m-30) REVERT: E 211 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6443 (mp) REVERT: E 212 SER cc_start: 0.7240 (t) cc_final: 0.6913 (p) REVERT: E 213 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5002 (t0) REVERT: E 310 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7065 (tt) REVERT: E 311 PRO cc_start: 0.7131 (Cg_endo) cc_final: 0.6810 (Cg_exo) REVERT: E 348 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6525 (t70) REVERT: E 401 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8129 (mt) REVERT: E 429 HIS cc_start: 0.7367 (m90) cc_final: 0.7023 (m90) REVERT: E 473 CYS cc_start: 0.8495 (m) cc_final: 0.7993 (m) REVERT: E 535 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8168 (mt) outliers start: 83 outliers final: 34 residues processed: 201 average time/residue: 0.6569 time to fit residues: 143.0166 Evaluate side-chains 190 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.177866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121139 restraints weight = 12331.894| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.34 r_work: 0.3150 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12445 Z= 0.193 Angle : 0.594 8.123 16871 Z= 0.302 Chirality : 0.046 0.287 1850 Planarity : 0.004 0.037 2170 Dihedral : 9.101 90.281 1734 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 6.49 % Allowed : 24.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1512 helix: 0.98 (0.23), residues: 506 sheet: 0.31 (0.28), residues: 348 loop : -1.24 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.018 0.002 TYR B 135 PHE 0.015 0.002 PHE E 437 TRP 0.014 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00478 (12443) covalent geometry : angle 0.59357 (16871) hydrogen bonds : bond 0.04381 ( 520) hydrogen bonds : angle 4.79628 ( 1440) Misc. bond : bond 0.00232 ( 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 227 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 141 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7457 (t0) cc_final: 0.6982 (m-30) REVERT: A 90 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6955 (mtmp) REVERT: A 290 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7372 (mtpp) REVERT: B 27 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4944 (mmt) REVERT: B 38 LYS cc_start: 0.8763 (ttpp) cc_final: 0.7513 (tptt) REVERT: B 50 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 87 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6159 (tmt170) REVERT: B 100 ARG cc_start: 0.4353 (OUTLIER) cc_final: 0.3352 (mmm160) REVERT: B 133 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: B 223 GLU cc_start: 0.6727 (tp30) cc_final: 0.6370 (tp30) REVERT: B 275 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6754 (t) REVERT: B 335 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7362 (p0) REVERT: B 401 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 404 GLU cc_start: 0.7856 (tp30) cc_final: 0.7464 (tt0) REVERT: B 440 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6361 (mmm160) REVERT: B 528 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6694 (mp) REVERT: B 530 ASN cc_start: 0.7634 (m-40) cc_final: 0.7165 (t0) REVERT: D 75 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: E 48 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: E 51 MET cc_start: 0.6844 (mtp) cc_final: 0.6402 (mtt) REVERT: E 71 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: E 101 VAL cc_start: 0.7670 (t) cc_final: 0.7380 (p) REVERT: E 190 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6369 (tt) REVERT: E 192 GLN cc_start: 0.6120 (mt0) cc_final: 0.5877 (tt0) REVERT: E 211 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6429 (mp) REVERT: E 212 SER cc_start: 0.7264 (t) cc_final: 0.6975 (p) REVERT: E 272 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7371 (p) REVERT: E 310 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7098 (tt) REVERT: E 311 PRO cc_start: 0.7075 (Cg_endo) cc_final: 0.6767 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7695 (ptm-80) cc_final: 0.7001 (mtp-110) REVERT: E 348 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6477 (t70) REVERT: E 401 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8118 (mt) REVERT: E 429 HIS cc_start: 0.7352 (m90) cc_final: 0.6995 (m90) REVERT: E 473 CYS cc_start: 0.8484 (m) cc_final: 0.7930 (m) outliers start: 86 outliers final: 39 residues processed: 204 average time/residue: 0.6421 time to fit residues: 142.0775 Evaluate side-chains 198 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 290 LYS 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 76 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 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 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 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 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.0170 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.0370 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 292 GLN E 184 HIS E 201 HIS E 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.185396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135499 restraints weight = 12104.603| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.19 r_work: 0.3271 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1315 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= 0.090 Angle : 0.473 7.421 16871 Z= 0.248 Chirality : 0.042 0.212 1850 Planarity : 0.003 0.035 2170 Dihedral : 8.636 88.121 1731 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 4.00 % Allowed : 27.02 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.21), residues: 1512 helix: 1.43 (0.23), residues: 507 sheet: 0.41 (0.28), residues: 350 loop : -1.15 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 40 TYR 0.014 0.001 TYR A 304 PHE 0.011 0.001 PHE E 85 TRP 0.015 0.001 TRP B 168 HIS 0.007 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00200 (12443) covalent geometry : angle 0.47301 (16871) hydrogen bonds : bond 0.03203 ( 520) hydrogen bonds : angle 4.52244 ( 1440) Misc. bond : bond 0.00071 ( 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 202 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7464 (t0) cc_final: 0.7126 (m-30) REVERT: A 75 LYS cc_start: 0.7861 (ttpp) cc_final: 0.7580 (mtpp) REVERT: A 90 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7156 (mtmp) REVERT: A 163 GLU cc_start: 0.8189 (tp30) cc_final: 0.7920 (tm-30) REVERT: B 27 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4862 (mmt) REVERT: B 38 LYS cc_start: 0.8781 (ttpp) cc_final: 0.7670 (tptt) REVERT: B 51 MET cc_start: 0.7300 (mtp) cc_final: 0.6878 (mtt) REVERT: B 87 ARG cc_start: 0.7311 (ttm170) cc_final: 0.6431 (tmt170) REVERT: B 129 GLU cc_start: 0.7471 (mp0) cc_final: 0.7055 (mp0) REVERT: B 133 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 223 GLU cc_start: 0.6758 (tp30) cc_final: 0.6432 (tp30) REVERT: B 275 CYS cc_start: 0.7470 (m) cc_final: 0.6891 (t) REVERT: B 335 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.6963 (p0) REVERT: B 401 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 404 GLU cc_start: 0.7802 (tp30) cc_final: 0.7550 (tt0) REVERT: B 440 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7283 (ptm-80) REVERT: B 528 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6655 (mp) REVERT: B 530 ASN cc_start: 0.7737 (m-40) cc_final: 0.7384 (t0) REVERT: E 51 MET cc_start: 0.7014 (mtp) cc_final: 0.6659 (mtt) REVERT: E 192 GLN cc_start: 0.6128 (mt0) cc_final: 0.5771 (tt0) REVERT: E 211 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6577 (mp) REVERT: E 212 SER cc_start: 0.7259 (t) cc_final: 0.6963 (p) REVERT: E 213 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5291 (t70) REVERT: E 310 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7099 (tt) REVERT: E 311 PRO cc_start: 0.7054 (Cg_endo) cc_final: 0.6762 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7764 (ptm-80) cc_final: 0.7274 (mtp-110) REVERT: E 429 HIS cc_start: 0.7324 (m90) cc_final: 0.7061 (m90) outliers start: 53 outliers final: 25 residues processed: 192 average time/residue: 0.7011 time to fit residues: 145.3166 Evaluate side-chains 173 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 76 ARG Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 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 401 LEU Chi-restraints excluded: chain B residue 437 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 81 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.4028 r_free = 0.4028 target = 0.182646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133786 restraints weight = 12152.823| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.21 r_work: 0.3205 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1322 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= 0.154 Angle : 0.543 7.703 16871 Z= 0.279 Chirality : 0.045 0.265 1850 Planarity : 0.004 0.035 2170 Dihedral : 8.474 89.014 1723 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 4.53 % Allowed : 26.42 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1512 helix: 1.32 (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 ARG 0.004 0.000 ARG A 56 TYR 0.018 0.002 TYR B 135 PHE 0.013 0.001 PHE E 437 TRP 0.014 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00380 (12443) covalent geometry : angle 0.54306 (16871) hydrogen bonds : bond 0.03884 ( 520) hydrogen bonds : angle 4.62815 ( 1440) Misc. bond : bond 0.00184 ( 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 200 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7496 (t0) cc_final: 0.7183 (m-30) REVERT: A 75 LYS cc_start: 0.7990 (ttpp) cc_final: 0.7685 (mtpp) REVERT: A 90 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7218 (mtmp) REVERT: B 38 LYS cc_start: 0.8831 (ttpp) cc_final: 0.7768 (tptt) REVERT: B 51 MET cc_start: 0.7286 (mtp) cc_final: 0.6897 (mtt) REVERT: B 87 ARG cc_start: 0.7419 (ttm170) cc_final: 0.6609 (tmt170) REVERT: B 100 ARG cc_start: 0.4454 (OUTLIER) cc_final: 0.3580 (mmm160) REVERT: B 133 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: B 223 GLU cc_start: 0.6793 (tp30) cc_final: 0.6507 (tp30) REVERT: B 255 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.7086 (t-90) REVERT: B 275 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7092 (t) REVERT: B 335 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7277 (p0) REVERT: B 401 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8510 (mt) REVERT: B 404 GLU cc_start: 0.7847 (tp30) cc_final: 0.7589 (tt0) REVERT: B 440 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7374 (ptm-80) REVERT: B 528 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6880 (mp) REVERT: B 530 ASN cc_start: 0.7771 (m-40) cc_final: 0.7437 (t0) REVERT: E 51 MET cc_start: 0.7069 (mtp) cc_final: 0.6693 (mtt) REVERT: E 101 VAL cc_start: 0.7857 (t) cc_final: 0.7493 (p) REVERT: E 192 GLN cc_start: 0.6268 (mt0) cc_final: 0.5987 (tt0) REVERT: E 211 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6679 (mp) REVERT: E 212 SER cc_start: 0.7410 (t) cc_final: 0.7112 (p) REVERT: E 213 ASP cc_start: 0.5663 (OUTLIER) cc_final: 0.5343 (t70) REVERT: E 272 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7688 (p) REVERT: E 310 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7126 (tt) REVERT: E 311 PRO cc_start: 0.7135 (Cg_endo) cc_final: 0.6813 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7807 (ptm-80) cc_final: 0.7292 (mtp-110) REVERT: E 401 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (mt) REVERT: E 429 HIS cc_start: 0.7418 (m90) cc_final: 0.7156 (m90) outliers start: 60 outliers final: 31 residues processed: 188 average time/residue: 0.6733 time to fit residues: 137.0798 Evaluate side-chains 184 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 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 275 CYS 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 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 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 145 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 255 HIS B 292 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS E 201 HIS E 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.183357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127631 restraints weight = 12108.461| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.30 r_work: 0.3262 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12445 Z= 0.130 Angle : 0.522 7.657 16871 Z= 0.269 Chirality : 0.044 0.250 1850 Planarity : 0.003 0.035 2170 Dihedral : 8.457 89.075 1723 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 4.38 % Allowed : 26.64 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1512 helix: 1.35 (0.23), residues: 501 sheet: 0.35 (0.28), residues: 350 loop : -1.14 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 127 TYR 0.017 0.001 TYR B 135 PHE 0.012 0.001 PHE E 437 TRP 0.016 0.001 TRP B 168 HIS 0.008 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00313 (12443) covalent geometry : angle 0.52207 (16871) hydrogen bonds : bond 0.03689 ( 520) hydrogen bonds : angle 4.60247 ( 1440) Misc. bond : bond 0.00158 ( 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 194 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7478 (t0) cc_final: 0.7013 (m-30) REVERT: A 75 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7330 (mtpp) REVERT: A 90 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6933 (mtmp) REVERT: A 163 GLU cc_start: 0.8331 (tp30) cc_final: 0.8031 (tm-30) REVERT: A 253 TYR cc_start: 0.8807 (t80) cc_final: 0.8570 (t80) REVERT: B 27 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4961 (mmt) REVERT: B 38 LYS cc_start: 0.8772 (ttpp) cc_final: 0.7573 (tptt) REVERT: B 51 MET cc_start: 0.7080 (mtp) cc_final: 0.6653 (mtt) REVERT: B 87 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6208 (tmt170) REVERT: B 100 ARG cc_start: 0.4367 (OUTLIER) cc_final: 0.3563 (mmm160) REVERT: B 255 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: B 275 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6975 (t) REVERT: B 335 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7213 (p0) REVERT: B 401 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 404 GLU cc_start: 0.7910 (tp30) cc_final: 0.7558 (tt0) REVERT: B 528 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6700 (mp) REVERT: B 530 ASN cc_start: 0.7626 (m-40) cc_final: 0.7204 (t0) REVERT: D 75 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: E 51 MET cc_start: 0.6816 (mtp) cc_final: 0.6402 (mtt) REVERT: E 192 GLN cc_start: 0.6068 (mt0) cc_final: 0.5805 (tt0) REVERT: E 211 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6407 (mp) REVERT: E 212 SER cc_start: 0.7240 (t) cc_final: 0.6911 (p) REVERT: E 213 ASP cc_start: 0.5602 (OUTLIER) cc_final: 0.5271 (t70) REVERT: E 272 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7536 (p) REVERT: E 310 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7079 (tt) REVERT: E 311 PRO cc_start: 0.7031 (Cg_endo) cc_final: 0.6729 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7646 (ptm-80) cc_final: 0.7034 (mtp-110) REVERT: E 348 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6370 (t70) REVERT: E 401 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8175 (mt) REVERT: E 429 HIS cc_start: 0.7305 (m90) cc_final: 0.6985 (m90) outliers start: 58 outliers final: 32 residues processed: 183 average time/residue: 0.6726 time to fit residues: 133.1179 Evaluate side-chains 183 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 160 VAL 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 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 503 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 84 CYS 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 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 255 HIS B 292 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS E 201 HIS E 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.182690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133238 restraints weight = 12164.631| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.27 r_work: 0.3217 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1372 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= 0.149 Angle : 0.545 7.815 16871 Z= 0.280 Chirality : 0.045 0.261 1850 Planarity : 0.004 0.046 2170 Dihedral : 8.493 89.401 1722 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 4.53 % Allowed : 26.79 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.21), residues: 1512 helix: 1.28 (0.23), residues: 501 sheet: 0.25 (0.28), residues: 343 loop : -1.12 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 45 TYR 0.018 0.002 TYR B 135 PHE 0.013 0.001 PHE E 437 TRP 0.015 0.001 TRP B 168 HIS 0.009 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00363 (12443) covalent geometry : angle 0.54488 (16871) hydrogen bonds : bond 0.03865 ( 520) hydrogen bonds : angle 4.64388 ( 1440) Misc. bond : bond 0.00180 ( 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 198 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7470 (t0) cc_final: 0.7155 (m-30) REVERT: A 90 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7168 (mtmp) REVERT: B 27 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4902 (mmt) REVERT: B 38 LYS cc_start: 0.8810 (ttpp) cc_final: 0.7731 (tptt) REVERT: B 51 MET cc_start: 0.7232 (mtp) cc_final: 0.6858 (mtt) REVERT: B 87 ARG cc_start: 0.7383 (ttm170) cc_final: 0.6562 (tmt170) REVERT: B 100 ARG cc_start: 0.4370 (OUTLIER) cc_final: 0.3501 (mmm160) REVERT: B 129 GLU cc_start: 0.7637 (mp0) cc_final: 0.7274 (mp0) REVERT: B 255 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6806 (t-90) REVERT: B 275 CYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7024 (t) REVERT: B 335 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7308 (p0) REVERT: B 401 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8526 (mt) REVERT: B 404 GLU cc_start: 0.7819 (tp30) cc_final: 0.7558 (tt0) REVERT: B 528 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6811 (mp) REVERT: B 530 ASN cc_start: 0.7720 (m-40) cc_final: 0.7392 (t0) REVERT: D 75 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: E 51 MET cc_start: 0.7009 (mtp) cc_final: 0.6629 (mtt) REVERT: E 101 VAL cc_start: 0.7791 (t) cc_final: 0.7467 (p) REVERT: E 192 GLN cc_start: 0.6231 (mt0) cc_final: 0.6002 (tt0) REVERT: E 211 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6669 (mp) REVERT: E 212 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.7078 (p) REVERT: E 213 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.5358 (t70) REVERT: E 272 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7703 (p) REVERT: E 310 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7118 (tt) REVERT: E 311 PRO cc_start: 0.7102 (Cg_endo) cc_final: 0.6794 (Cg_exo) REVERT: E 314 ARG cc_start: 0.7726 (ptm-80) cc_final: 0.7210 (mtp-110) REVERT: E 348 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6486 (t70) REVERT: E 401 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8312 (mt) REVERT: E 429 HIS cc_start: 0.7383 (m90) cc_final: 0.7118 (m90) outliers start: 60 outliers final: 36 residues processed: 185 average time/residue: 0.6494 time to fit residues: 130.0282 Evaluate side-chains 191 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 256 SER 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 76 ARG 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 160 VAL 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 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 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 B residue 535 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 168 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 212 SER 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 284 SER Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 521 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 60 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 255 HIS B 292 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS E 201 HIS E 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.182921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133312 restraints weight = 12040.445| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.21 r_work: 0.3222 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1370 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= 0.141 Angle : 0.539 7.801 16871 Z= 0.278 Chirality : 0.045 0.254 1850 Planarity : 0.004 0.049 2170 Dihedral : 8.468 89.449 1722 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 4.23 % Allowed : 26.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.21), residues: 1512 helix: 1.30 (0.23), residues: 501 sheet: 0.24 (0.28), residues: 343 loop : -1.13 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 45 TYR 0.017 0.001 TYR B 135 PHE 0.013 0.001 PHE E 437 TRP 0.015 0.001 TRP B 168 HIS 0.009 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00342 (12443) covalent geometry : angle 0.53914 (16871) hydrogen bonds : bond 0.03791 ( 520) hydrogen bonds : angle 4.63937 ( 1440) Misc. bond : bond 0.00168 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4944.41 seconds wall clock time: 85 minutes 10.33 seconds (5110.33 seconds total)