Starting phenix.real_space_refine on Sun Jun 8 16:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uts_42548/06_2025/8uts_42548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uts_42548/06_2025/8uts_42548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uts_42548/06_2025/8uts_42548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uts_42548/06_2025/8uts_42548.map" model { file = "/net/cci-nas-00/data/ceres_data/8uts_42548/06_2025/8uts_42548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uts_42548/06_2025/8uts_42548.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 6098 2.51 5 N 1671 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9748 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2781 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 12, 'TRANS': 341} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.64, per 1000 atoms: 0.78 Number of scatterers: 9748 At special positions: 0 Unit cell: (106.872, 76.212, 112.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 5 15.00 Mg 1 11.99 O 1908 8.00 N 1671 7.00 C 6098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 47.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 88 Processing helix chain 'K' and resid 102 through 108 removed outlier: 3.554A pdb=" N THR K 106 " --> pdb=" O GLY K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 133 removed outlier: 3.607A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.672A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.529A pdb=" N LEU K 315 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.923A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.950A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.342A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.066A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.824A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.507A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.140A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.726A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.503A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.611A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.056A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.039A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.995A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.224A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.788A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.754A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.046A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.590A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.875A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.822A pdb=" N VAL B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.604A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.356A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.751A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.507A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER K 5 " --> pdb=" O SER K 323 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG K 324 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL K 154 " --> pdb=" O LEU K 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.507A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER K 5 " --> pdb=" O SER K 323 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG K 324 " --> pdb=" O ASN K 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 removed outlier: 3.555A pdb=" N ALA K 206 " --> pdb=" O SER K 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.937A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.199A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.767A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 53 498 hydrogen bonds defined for protein. 1422 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: 3.14 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1785 1.32 - 1.45: 2561 1.45 - 1.57: 5491 1.57 - 1.70: 12 1.70 - 1.82: 105 Bond restraints: 9954 Sorted by residual: bond pdb=" N THR B 429 " pdb=" CA THR B 429 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.12e+01 bond pdb=" N VAL K 38 " pdb=" CA VAL K 38 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.22e-02 6.72e+03 1.01e+01 bond pdb=" N TYR B 422 " pdb=" CA TYR B 422 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.55e+00 bond pdb=" N LYS K 296 " pdb=" CA LYS K 296 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.29e+00 bond pdb=" N LEU B 263 " pdb=" CA LEU B 263 " ideal model delta sigma weight residual 1.464 1.503 -0.039 1.30e-02 5.92e+03 9.04e+00 ... (remaining 9949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12962 1.95 - 3.90: 435 3.90 - 5.85: 91 5.85 - 7.80: 14 7.80 - 9.75: 2 Bond angle restraints: 13504 Sorted by residual: angle pdb=" C PHE B 260 " pdb=" CA PHE B 260 " pdb=" CB PHE B 260 " ideal model delta sigma weight residual 108.91 116.62 -7.71 1.53e+00 4.27e-01 2.54e+01 angle pdb=" CA LYS K 25 " pdb=" CB LYS K 25 " pdb=" CG LYS K 25 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" N ASP B 427 " pdb=" CA ASP B 427 " pdb=" C ASP B 427 " ideal model delta sigma weight residual 113.97 108.07 5.90 1.28e+00 6.10e-01 2.13e+01 angle pdb=" CA ASN K 295 " pdb=" C ASN K 295 " pdb=" O ASN K 295 " ideal model delta sigma weight residual 121.00 116.49 4.51 1.05e+00 9.07e-01 1.85e+01 angle pdb=" CA LEU B 263 " pdb=" C LEU B 263 " pdb=" O LEU B 263 " ideal model delta sigma weight residual 122.63 117.43 5.20 1.29e+00 6.01e-01 1.62e+01 ... (remaining 13499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 5727 30.68 - 61.36: 287 61.36 - 92.04: 31 92.04 - 122.72: 3 122.72 - 153.40: 11 Dihedral angle restraints: 6059 sinusoidal: 2502 harmonic: 3557 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -48.81 153.40 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -51.21 120.47 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" CA ALA B 54 " pdb=" C ALA B 54 " pdb=" N THR B 55 " pdb=" CA THR B 55 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 6056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1182 0.052 - 0.104: 225 0.104 - 0.156: 69 0.156 - 0.208: 5 0.208 - 0.261: 2 Chirality restraints: 1483 Sorted by residual: chirality pdb=" CB THR B 149 " pdb=" CA THR B 149 " pdb=" OG1 THR B 149 " pdb=" CG2 THR B 149 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE K 304 " pdb=" N ILE K 304 " pdb=" C ILE K 304 " pdb=" CB ILE K 304 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1480 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO K 292 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 45 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C GLU K 45 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU K 45 " 0.023 2.00e-02 2.50e+03 pdb=" N THR K 46 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 36 " -0.014 2.00e-02 2.50e+03 2.19e-02 9.57e+00 pdb=" CG TYR B 36 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 36 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 36 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 36 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 36 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 36 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 36 " -0.000 2.00e-02 2.50e+03 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 74 2.57 - 3.16: 7756 3.16 - 3.74: 14623 3.74 - 4.32: 20059 4.32 - 4.90: 34619 Nonbonded interactions: 77131 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR A 145 " pdb=" O2G GTP A 501 " model vdw 2.071 3.040 nonbonded pdb=" O TYR K 89 " pdb=" OG SER K 242 " model vdw 2.147 3.040 nonbonded pdb=" O ASN B 226 " pdb=" OG SER B 230 " model vdw 2.176 3.040 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.201 2.170 ... (remaining 77126 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.005 0.045 9954 Z= 0.253 Angle : 0.836 9.747 13504 Z= 0.462 Chirality : 0.047 0.261 1483 Planarity : 0.006 0.098 1757 Dihedral : 18.949 153.404 3775 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.41 % Favored : 93.78 % Rotamer: Outliers : 2.56 % Allowed : 20.17 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1221 helix: 1.35 (0.23), residues: 483 sheet: -0.19 (0.35), residues: 211 loop : -1.56 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 344 HIS 0.004 0.001 HIS A 28 PHE 0.032 0.002 PHE A 267 TYR 0.051 0.002 TYR B 36 ARG 0.008 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.16624 ( 460) hydrogen bonds : angle 6.13265 ( 1422) covalent geometry : bond 0.00475 ( 9954) covalent geometry : angle 0.83571 (13504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 229 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7037 (tpt170) REVERT: K 356 CYS cc_start: 0.3532 (OUTLIER) cc_final: 0.3307 (p) REVERT: A 432 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6653 (t80) REVERT: B 299 MET cc_start: 0.7734 (mpp) cc_final: 0.7454 (mtt) REVERT: B 432 GLU cc_start: 0.0904 (OUTLIER) cc_final: 0.0203 (pm20) outliers start: 27 outliers final: 7 residues processed: 206 average time/residue: 1.1483 time to fit residues: 254.0056 Evaluate side-chains 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 356 CYS Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 0.0970 chunk 110 optimal weight: 6.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 192 HIS A 356 ASN B 165 ASN B 245 GLN B 280 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053396 restraints weight = 29245.274| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.38 r_work: 0.2959 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9954 Z= 0.183 Angle : 0.664 9.205 13504 Z= 0.338 Chirality : 0.047 0.283 1483 Planarity : 0.006 0.097 1757 Dihedral : 13.301 145.911 1484 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.42 % Favored : 95.25 % Rotamer: Outliers : 5.21 % Allowed : 20.45 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1221 helix: 1.54 (0.23), residues: 504 sheet: 0.20 (0.35), residues: 211 loop : -1.47 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.015 0.002 HIS A 192 PHE 0.014 0.002 PHE A 149 TYR 0.016 0.002 TYR K 67 ARG 0.005 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 460) hydrogen bonds : angle 4.73986 ( 1422) covalent geometry : bond 0.00413 ( 9954) covalent geometry : angle 0.66415 (13504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 87 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 138 MET cc_start: 0.7279 (mpp) cc_final: 0.6153 (mpm) REVERT: A 108 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.5422 (p90) REVERT: A 211 ASP cc_start: 0.8908 (m-30) cc_final: 0.8640 (t70) REVERT: A 239 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8847 (t) REVERT: A 432 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6439 (t80) REVERT: B 1 MET cc_start: 0.6938 (mmp) cc_final: 0.6731 (mmp) REVERT: B 197 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 209 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8536 (t0) REVERT: B 257 MET cc_start: 0.8499 (mmm) cc_final: 0.8186 (mmm) REVERT: B 363 MET cc_start: 0.9083 (ptp) cc_final: 0.8768 (ptt) REVERT: B 432 GLU cc_start: 0.1440 (OUTLIER) cc_final: 0.1159 (tt0) outliers start: 55 outliers final: 12 residues processed: 137 average time/residue: 1.0780 time to fit residues: 160.1487 Evaluate side-chains 87 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 118 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN A 356 ASN B 137 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.066073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051600 restraints weight = 30111.450| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.40 r_work: 0.2925 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 9954 Z= 0.227 Angle : 0.681 10.340 13504 Z= 0.347 Chirality : 0.048 0.410 1483 Planarity : 0.006 0.094 1757 Dihedral : 10.615 145.507 1478 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer: Outliers : 4.55 % Allowed : 21.69 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1221 helix: 1.44 (0.23), residues: 503 sheet: 0.26 (0.36), residues: 214 loop : -1.67 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.008 0.002 HIS A 192 PHE 0.019 0.002 PHE A 149 TYR 0.018 0.002 TYR K 67 ARG 0.004 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 460) hydrogen bonds : angle 4.84544 ( 1422) covalent geometry : bond 0.00515 ( 9954) covalent geometry : angle 0.68094 (13504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 75 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 138 MET cc_start: 0.7341 (mpp) cc_final: 0.6598 (mpm) REVERT: A 211 ASP cc_start: 0.8981 (m-30) cc_final: 0.8751 (t70) REVERT: A 432 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 197 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: B 209 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8863 (t70) REVERT: B 363 MET cc_start: 0.9096 (ptp) cc_final: 0.8721 (ptt) REVERT: B 432 GLU cc_start: 0.1155 (OUTLIER) cc_final: 0.0708 (pt0) outliers start: 48 outliers final: 18 residues processed: 119 average time/residue: 1.1926 time to fit residues: 154.5636 Evaluate side-chains 90 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 114 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052021 restraints weight = 29965.534| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.42 r_work: 0.2940 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9954 Z= 0.163 Angle : 0.615 9.506 13504 Z= 0.311 Chirality : 0.046 0.369 1483 Planarity : 0.005 0.089 1757 Dihedral : 9.332 143.579 1478 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer: Outliers : 4.83 % Allowed : 21.50 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1221 helix: 1.66 (0.24), residues: 503 sheet: 0.42 (0.35), residues: 221 loop : -1.66 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 192 PHE 0.018 0.002 PHE A 149 TYR 0.016 0.002 TYR K 67 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 460) hydrogen bonds : angle 4.62759 ( 1422) covalent geometry : bond 0.00368 ( 9954) covalent geometry : angle 0.61536 (13504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 76 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: K 138 MET cc_start: 0.7248 (mpp) cc_final: 0.6636 (mpm) REVERT: K 294 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4840 (pttt) REVERT: A 108 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6504 (p90) REVERT: A 230 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9066 (mt) REVERT: A 367 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: A 432 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6567 (t80) REVERT: B 67 ASP cc_start: 0.8721 (t0) cc_final: 0.8371 (t0) REVERT: B 197 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: B 209 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8842 (t70) REVERT: B 291 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8306 (tp-100) REVERT: B 311 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 432 GLU cc_start: 0.1136 (OUTLIER) cc_final: 0.0456 (pt0) outliers start: 51 outliers final: 19 residues processed: 120 average time/residue: 1.5408 time to fit residues: 203.9559 Evaluate side-chains 92 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 294 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 301 GLN A 356 ASN B 131 GLN B 332 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051445 restraints weight = 29962.287| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.38 r_work: 0.2926 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9954 Z= 0.207 Angle : 0.640 9.710 13504 Z= 0.329 Chirality : 0.046 0.262 1483 Planarity : 0.005 0.088 1757 Dihedral : 9.485 143.971 1478 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 5.21 % Allowed : 21.50 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.24), residues: 1221 helix: 1.49 (0.23), residues: 503 sheet: 0.27 (0.34), residues: 221 loop : -1.75 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS B 190 PHE 0.020 0.002 PHE A 149 TYR 0.015 0.002 TYR A 172 ARG 0.003 0.001 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 460) hydrogen bonds : angle 4.74636 ( 1422) covalent geometry : bond 0.00470 ( 9954) covalent geometry : angle 0.64023 (13504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 67 time to evaluate : 1.182 Fit side-chains REVERT: K 294 LYS cc_start: 0.5199 (OUTLIER) cc_final: 0.4911 (pttt) REVERT: A 230 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9066 (mt) REVERT: A 367 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 432 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6544 (t80) REVERT: B 31 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: B 67 ASP cc_start: 0.8786 (t0) cc_final: 0.8435 (t0) REVERT: B 197 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: B 209 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8834 (t70) REVERT: B 291 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8303 (tp-100) REVERT: B 432 GLU cc_start: 0.0823 (OUTLIER) cc_final: 0.0218 (pt0) outliers start: 55 outliers final: 29 residues processed: 118 average time/residue: 0.9553 time to fit residues: 123.7904 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 294 LYS Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 193 GLN A 356 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.051827 restraints weight = 29914.612| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.33 r_work: 0.2936 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9954 Z= 0.186 Angle : 0.626 12.413 13504 Z= 0.317 Chirality : 0.046 0.255 1483 Planarity : 0.005 0.087 1757 Dihedral : 9.399 143.744 1478 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 4.83 % Allowed : 22.16 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1221 helix: 1.54 (0.23), residues: 503 sheet: 0.16 (0.34), residues: 221 loop : -1.72 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.019 0.002 PHE A 149 TYR 0.014 0.002 TYR K 146 ARG 0.003 0.000 ARG K 316 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 460) hydrogen bonds : angle 4.66820 ( 1422) covalent geometry : bond 0.00422 ( 9954) covalent geometry : angle 0.62608 (13504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 63 time to evaluate : 1.163 Fit side-chains REVERT: A 230 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9062 (mt) REVERT: A 432 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6544 (t80) REVERT: B 31 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: B 67 ASP cc_start: 0.8781 (t0) cc_final: 0.8229 (t0) REVERT: B 73 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7525 (mpt) REVERT: B 197 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: B 209 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8842 (t70) REVERT: B 291 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8304 (tp-100) REVERT: B 432 GLU cc_start: 0.0783 (OUTLIER) cc_final: 0.0364 (pt0) outliers start: 51 outliers final: 25 residues processed: 109 average time/residue: 0.9917 time to fit residues: 118.2620 Evaluate side-chains 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051864 restraints weight = 30242.043| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.39 r_work: 0.2942 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9954 Z= 0.164 Angle : 0.598 10.239 13504 Z= 0.304 Chirality : 0.045 0.253 1483 Planarity : 0.005 0.087 1757 Dihedral : 9.301 143.702 1478 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.92 % Rotamer: Outliers : 4.26 % Allowed : 22.82 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1221 helix: 1.63 (0.23), residues: 503 sheet: 0.21 (0.34), residues: 220 loop : -1.73 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 88 PHE 0.018 0.001 PHE A 149 TYR 0.011 0.001 TYR K 67 ARG 0.003 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 460) hydrogen bonds : angle 4.57747 ( 1422) covalent geometry : bond 0.00371 ( 9954) covalent geometry : angle 0.59806 (13504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 63 time to evaluate : 1.185 Fit side-chains REVERT: A 230 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9060 (mt) REVERT: A 432 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6556 (t80) REVERT: B 31 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: B 67 ASP cc_start: 0.8778 (t0) cc_final: 0.8247 (t0) REVERT: B 73 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7562 (mpt) REVERT: B 197 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: B 209 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8832 (t70) REVERT: B 432 GLU cc_start: 0.0779 (OUTLIER) cc_final: 0.0320 (pt0) outliers start: 45 outliers final: 27 residues processed: 103 average time/residue: 0.9877 time to fit residues: 111.5452 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 227 GLN A 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051270 restraints weight = 30400.822| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.37 r_work: 0.2927 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9954 Z= 0.221 Angle : 0.663 10.568 13504 Z= 0.336 Chirality : 0.046 0.259 1483 Planarity : 0.005 0.088 1757 Dihedral : 9.502 145.019 1476 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 4.17 % Allowed : 23.30 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1221 helix: 1.44 (0.23), residues: 502 sheet: 0.05 (0.35), residues: 218 loop : -1.78 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 21 HIS 0.005 0.001 HIS B 190 PHE 0.020 0.002 PHE A 149 TYR 0.016 0.002 TYR A 172 ARG 0.005 0.001 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 460) hydrogen bonds : angle 4.77369 ( 1422) covalent geometry : bond 0.00503 ( 9954) covalent geometry : angle 0.66279 (13504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 1.148 Fit side-chains REVERT: A 230 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9074 (mt) REVERT: A 432 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6593 (t80) REVERT: B 31 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: B 67 ASP cc_start: 0.8825 (t0) cc_final: 0.8286 (t0) REVERT: B 73 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7526 (mpt) REVERT: B 197 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: B 209 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8824 (t70) REVERT: B 432 GLU cc_start: 0.0816 (OUTLIER) cc_final: 0.0462 (pt0) outliers start: 44 outliers final: 29 residues processed: 104 average time/residue: 1.0081 time to fit residues: 114.5802 Evaluate side-chains 96 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.067348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.052762 restraints weight = 29888.677| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.41 r_work: 0.2968 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9954 Z= 0.118 Angle : 0.582 12.237 13504 Z= 0.291 Chirality : 0.044 0.242 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.090 144.730 1476 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 3.03 % Allowed : 24.34 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1221 helix: 1.78 (0.24), residues: 504 sheet: 0.27 (0.35), residues: 225 loop : -1.67 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS B 396 PHE 0.017 0.001 PHE A 149 TYR 0.008 0.001 TYR K 67 ARG 0.003 0.000 ARG K 254 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 460) hydrogen bonds : angle 4.41921 ( 1422) covalent geometry : bond 0.00261 ( 9954) covalent geometry : angle 0.58169 (13504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 1.122 Fit side-chains REVERT: A 230 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9039 (mt) REVERT: A 432 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6521 (t80) REVERT: B 31 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: B 67 ASP cc_start: 0.8741 (t0) cc_final: 0.8389 (t0) REVERT: B 197 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 432 GLU cc_start: 0.0851 (OUTLIER) cc_final: 0.0427 (pt0) outliers start: 32 outliers final: 17 residues processed: 98 average time/residue: 1.3547 time to fit residues: 144.1497 Evaluate side-chains 82 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 GLN A 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.067457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053287 restraints weight = 29903.712| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.36 r_work: 0.2979 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9954 Z= 0.125 Angle : 0.617 13.107 13504 Z= 0.305 Chirality : 0.044 0.246 1483 Planarity : 0.005 0.086 1757 Dihedral : 8.924 142.774 1475 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 2.27 % Allowed : 25.47 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1221 helix: 1.87 (0.24), residues: 504 sheet: 0.33 (0.35), residues: 225 loop : -1.68 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS B 396 PHE 0.016 0.001 PHE A 149 TYR 0.007 0.001 TYR A 172 ARG 0.002 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 460) hydrogen bonds : angle 4.37216 ( 1422) covalent geometry : bond 0.00282 ( 9954) covalent geometry : angle 0.61686 (13504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 1.119 Fit side-chains REVERT: A 230 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9044 (mt) REVERT: A 432 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6550 (t80) REVERT: B 31 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: B 67 ASP cc_start: 0.8715 (t0) cc_final: 0.8354 (t0) REVERT: B 197 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: B 432 GLU cc_start: 0.0825 (OUTLIER) cc_final: 0.0336 (pt0) outliers start: 24 outliers final: 16 residues processed: 85 average time/residue: 1.1794 time to fit residues: 109.3214 Evaluate side-chains 82 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 56 optimal weight: 0.0370 chunk 121 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 356 ASN B 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.069277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054909 restraints weight = 29578.786| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.37 r_work: 0.3019 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9954 Z= 0.107 Angle : 0.599 11.646 13504 Z= 0.296 Chirality : 0.043 0.233 1483 Planarity : 0.005 0.085 1757 Dihedral : 8.596 139.428 1474 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 1.89 % Allowed : 25.85 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1221 helix: 2.07 (0.24), residues: 500 sheet: 0.70 (0.35), residues: 217 loop : -1.70 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS B 396 PHE 0.015 0.001 PHE A 149 TYR 0.010 0.001 TYR A 103 ARG 0.006 0.000 ARG K 75 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 460) hydrogen bonds : angle 4.21371 ( 1422) covalent geometry : bond 0.00234 ( 9954) covalent geometry : angle 0.59894 (13504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6042.48 seconds wall clock time: 106 minutes 49.05 seconds (6409.05 seconds total)