Starting phenix.real_space_refine on Fri Feb 14 04:19:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uts_42548/02_2025/8uts_42548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uts_42548/02_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_42548/02_2025/8uts_42548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uts_42548/02_2025/8uts_42548.map" model { file = "/net/cci-nas-00/data/ceres_data/8uts_42548/02_2025/8uts_42548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uts_42548/02_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-5592/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: 7.04, per 1000 atoms: 0.72 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 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: 1.09 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: 3.37 Time building geometry restraints manager: 2.69 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: 3.870 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- 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= 0.311 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 *********************** 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 : 1.074 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: 1.1942 time to fit residues: 264.3243 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 : 1.087 ------------------------------------------------------------------------------- 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 = 0.067579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053391 restraints weight = 29246.867| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.38 r_work: 0.2960 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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= 0.268 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 *********************** 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 : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 138 MET cc_start: 0.7282 (mpp) cc_final: 0.6162 (mpm) REVERT: A 108 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.5422 (p90) REVERT: A 211 ASP cc_start: 0.8900 (m-30) cc_final: 0.8636 (t70) REVERT: A 239 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8845 (t) REVERT: A 432 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6444 (t80) REVERT: B 1 MET cc_start: 0.6941 (mmp) cc_final: 0.6732 (mmp) REVERT: B 197 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: B 209 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8539 (t0) REVERT: B 257 MET cc_start: 0.8492 (mmm) cc_final: 0.8179 (mmm) REVERT: B 363 MET cc_start: 0.9081 (ptp) cc_final: 0.8767 (ptt) REVERT: B 432 GLU cc_start: 0.1444 (OUTLIER) cc_final: 0.1157 (tt0) outliers start: 55 outliers final: 12 residues processed: 137 average time/residue: 1.0649 time to fit residues: 158.2244 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 : 1.263 ------------------------------------------------------------------------------- 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: 0.0050 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 5.6002 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.066432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051939 restraints weight = 30078.326| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.42 r_work: 0.2933 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9954 Z= 0.297 Angle : 0.654 9.532 13504 Z= 0.333 Chirality : 0.047 0.418 1483 Planarity : 0.005 0.093 1757 Dihedral : 10.325 145.060 1478 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % 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: 0.10 (0.24), residues: 1221 helix: 1.54 (0.23), residues: 503 sheet: 0.31 (0.35), residues: 220 loop : -1.65 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.007 0.001 HIS A 192 PHE 0.019 0.002 PHE A 149 TYR 0.015 0.002 TYR K 67 ARG 0.004 0.001 ARG K 229 *********************** 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 125 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 77 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 138 MET cc_start: 0.7362 (mpp) cc_final: 0.6605 (mpm) REVERT: A 211 ASP cc_start: 0.8984 (m-30) cc_final: 0.8751 (t70) REVERT: A 432 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6564 (t80) REVERT: B 197 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: B 209 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8861 (t70) REVERT: B 363 MET cc_start: 0.9098 (ptp) cc_final: 0.8716 (ptt) REVERT: B 432 GLU cc_start: 0.1301 (OUTLIER) cc_final: 0.0722 (pt0) outliers start: 48 outliers final: 18 residues processed: 121 average time/residue: 1.1322 time to fit residues: 149.4275 Evaluate side-chains 89 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 332 ASN ** B 334 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 = 0.3432 r_free = 0.3432 target = 0.067022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052390 restraints weight = 29872.797| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.42 r_work: 0.2948 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9954 Z= 0.209 Angle : 0.600 11.650 13504 Z= 0.302 Chirality : 0.046 0.351 1483 Planarity : 0.005 0.088 1757 Dihedral : 9.237 143.023 1478 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 4.73 % Allowed : 21.21 % Favored : 74.05 % 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: 0.28 (0.24), residues: 1221 helix: 1.69 (0.23), residues: 509 sheet: 0.46 (0.35), residues: 221 loop : -1.62 (0.26), residues: 491 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 0.017 0.001 PHE A 149 TYR 0.014 0.001 TYR K 67 ARG 0.003 0.000 ARG B 306 *********************** 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 125 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 75 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 138 MET cc_start: 0.7250 (mpp) cc_final: 0.6619 (mpm) REVERT: K 294 LYS cc_start: 0.5241 (OUTLIER) cc_final: 0.4974 (pttt) REVERT: A 211 ASP cc_start: 0.8992 (m-30) cc_final: 0.8785 (t70) REVERT: A 230 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9072 (mt) REVERT: A 367 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: A 432 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6532 (t80) REVERT: B 67 ASP cc_start: 0.8708 (t0) cc_final: 0.8348 (t0) REVERT: B 197 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: B 209 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8872 (t70) REVERT: B 291 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8297 (tp-100) REVERT: B 311 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 363 MET cc_start: 0.9034 (ptp) cc_final: 0.8610 (ptt) REVERT: B 432 GLU cc_start: 0.1032 (OUTLIER) cc_final: 0.0378 (pt0) outliers start: 50 outliers final: 17 residues processed: 118 average time/residue: 1.0793 time to fit residues: 138.3938 Evaluate side-chains 90 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL 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 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 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: 2.9990 chunk 106 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 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 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.066115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051624 restraints weight = 29951.017| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.37 r_work: 0.2931 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9954 Z= 0.309 Angle : 0.636 9.703 13504 Z= 0.326 Chirality : 0.046 0.262 1483 Planarity : 0.005 0.088 1757 Dihedral : 9.444 144.013 1478 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.16 % Favored : 94.68 % Rotamer: Outliers : 4.64 % Allowed : 21.97 % Favored : 73.39 % 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: 0.09 (0.24), residues: 1221 helix: 1.62 (0.23), residues: 502 sheet: 0.34 (0.35), residues: 215 loop : -1.75 (0.25), residues: 504 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 0.019 0.002 PHE A 149 TYR 0.015 0.002 TYR A 172 ARG 0.003 0.001 ARG K 316 *********************** 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 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 67 time to evaluate : 1.182 Fit side-chains REVERT: K 138 MET cc_start: 0.7291 (mpp) cc_final: 0.6776 (mpm) REVERT: K 294 LYS cc_start: 0.5204 (OUTLIER) cc_final: 0.4916 (pttt) REVERT: A 230 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9073 (mt) REVERT: A 367 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: A 432 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6555 (t80) REVERT: B 31 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: B 67 ASP cc_start: 0.8778 (t0) cc_final: 0.8421 (t0) REVERT: B 197 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: B 209 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8846 (t70) REVERT: B 291 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8311 (tp-100) REVERT: B 432 GLU cc_start: 0.0829 (OUTLIER) cc_final: 0.0271 (pt0) outliers start: 49 outliers final: 23 residues processed: 112 average time/residue: 1.0193 time to fit residues: 125.0824 Evaluate side-chains 96 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 93 ILE 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 285 LEU Chi-restraints excluded: chain K residue 294 LYS Chi-restraints excluded: chain K residue 301 THR 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 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: 3.9990 chunk 16 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 193 GLN K 209 ASN A 356 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052646 restraints weight = 29824.737| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.38 r_work: 0.2958 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9954 Z= 0.194 Angle : 0.583 12.633 13504 Z= 0.292 Chirality : 0.044 0.248 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.163 141.888 1478 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.92 % Rotamer: Outliers : 4.07 % Allowed : 22.63 % 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: 0.31 (0.24), residues: 1221 helix: 1.82 (0.24), residues: 504 sheet: 0.47 (0.35), residues: 219 loop : -1.70 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS A 88 PHE 0.018 0.001 PHE A 149 TYR 0.011 0.001 TYR K 67 ARG 0.002 0.000 ARG K 316 *********************** 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 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 70 time to evaluate : 1.228 Fit side-chains REVERT: K 138 MET cc_start: 0.7225 (mpp) cc_final: 0.6708 (mpm) REVERT: K 294 LYS cc_start: 0.5223 (OUTLIER) cc_final: 0.4932 (pttt) REVERT: A 230 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9061 (mt) REVERT: A 432 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6516 (t80) REVERT: B 31 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: B 67 ASP cc_start: 0.8732 (t0) cc_final: 0.8368 (t0) REVERT: B 197 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: B 209 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8852 (t70) REVERT: B 291 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8308 (tp-100) REVERT: B 432 GLU cc_start: 0.0863 (OUTLIER) cc_final: 0.0310 (pt0) outliers start: 43 outliers final: 22 residues processed: 108 average time/residue: 1.0593 time to fit residues: 124.9761 Evaluate side-chains 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 93 ILE 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 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 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 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 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: 20.0000 chunk 1 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.066524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052266 restraints weight = 30195.032| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.36 r_work: 0.2950 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9954 Z= 0.236 Angle : 0.590 10.225 13504 Z= 0.298 Chirality : 0.044 0.253 1483 Planarity : 0.005 0.087 1757 Dihedral : 9.186 141.623 1478 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 4.26 % Allowed : 23.20 % 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: 0.24 (0.24), residues: 1221 helix: 1.79 (0.23), residues: 504 sheet: 0.39 (0.34), residues: 219 loop : -1.74 (0.25), residues: 498 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 0.018 0.001 PHE A 149 TYR 0.011 0.001 TYR K 67 ARG 0.003 0.000 ARG K 316 *********************** 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 : 1.250 Fit side-chains REVERT: K 138 MET cc_start: 0.7249 (mpp) cc_final: 0.6797 (mpm) REVERT: K 288 MET cc_start: 0.8403 (mtt) cc_final: 0.8201 (tpp) REVERT: A 230 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9069 (mt) REVERT: A 367 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 432 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6552 (t80) REVERT: B 31 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 67 ASP cc_start: 0.8755 (t0) cc_final: 0.8403 (t0) REVERT: B 197 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: B 209 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8844 (t70) REVERT: B 432 GLU cc_start: 0.0847 (OUTLIER) cc_final: 0.0357 (pt0) outliers start: 45 outliers final: 25 residues processed: 106 average time/residue: 1.0864 time to fit residues: 125.8444 Evaluate side-chains 96 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 314 LEU 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 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 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: 3.9990 chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.066848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052633 restraints weight = 30174.466| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.34 r_work: 0.2960 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9954 Z= 0.217 Angle : 0.595 13.244 13504 Z= 0.297 Chirality : 0.044 0.250 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.092 141.755 1477 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 4.26 % Allowed : 23.30 % Favored : 72.44 % 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: 0.24 (0.24), residues: 1221 helix: 1.78 (0.24), residues: 505 sheet: 0.43 (0.35), residues: 219 loop : -1.76 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS B 190 PHE 0.018 0.001 PHE A 149 TYR 0.010 0.001 TYR A 224 ARG 0.003 0.000 ARG A 79 *********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 1.196 Fit side-chains REVERT: A 230 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 367 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: A 432 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6569 (t80) REVERT: B 31 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: B 67 ASP cc_start: 0.8742 (t0) cc_final: 0.8387 (t0) REVERT: B 197 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: B 291 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8317 (tp-100) REVERT: B 432 GLU cc_start: 0.1049 (OUTLIER) cc_final: 0.0561 (pt0) outliers start: 45 outliers final: 27 residues processed: 104 average time/residue: 1.0557 time to fit residues: 120.1191 Evaluate side-chains 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain K residue 139 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 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 367 ASP 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 164 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 0.0570 chunk 76 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 4.3304 ------------------------------------------------------------------------------- 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 ** B 334 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 = 0.3429 r_free = 0.3429 target = 0.066589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052290 restraints weight = 30054.478| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.37 r_work: 0.2952 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9954 Z= 0.239 Angle : 0.599 11.803 13504 Z= 0.301 Chirality : 0.044 0.252 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.099 142.430 1475 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 4.36 % Allowed : 23.11 % 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: 0.21 (0.24), residues: 1221 helix: 1.77 (0.24), residues: 503 sheet: 0.41 (0.35), residues: 220 loop : -1.78 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.005 0.001 HIS B 190 PHE 0.018 0.001 PHE A 149 TYR 0.011 0.001 TYR K 146 ARG 0.004 0.000 ARG K 75 *********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 63 time to evaluate : 1.223 Fit side-chains REVERT: A 230 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9067 (mt) REVERT: A 432 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6563 (t80) REVERT: B 31 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: B 67 ASP cc_start: 0.8757 (t0) cc_final: 0.8402 (t0) REVERT: B 197 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: B 291 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8318 (tp-100) REVERT: B 432 GLU cc_start: 0.0925 (OUTLIER) cc_final: 0.0500 (pt0) outliers start: 46 outliers final: 28 residues processed: 104 average time/residue: 1.0753 time to fit residues: 122.1162 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 139 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 314 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.065941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051796 restraints weight = 30269.197| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.33 r_work: 0.2937 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9954 Z= 0.314 Angle : 0.660 12.710 13504 Z= 0.332 Chirality : 0.046 0.258 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.360 145.108 1475 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 3.69 % Allowed : 23.77 % 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: -0.04 (0.24), residues: 1221 helix: 1.56 (0.24), residues: 502 sheet: 0.08 (0.36), residues: 215 loop : -1.77 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.019 0.002 PHE A 149 TYR 0.018 0.002 TYR K 146 ARG 0.007 0.001 ARG K 75 ********************** 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 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 66 time to evaluate : 1.145 Fit side-chains REVERT: A 230 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9069 (mt) REVERT: A 367 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: A 432 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.6578 (t80) REVERT: B 31 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: B 67 ASP cc_start: 0.8816 (t0) cc_final: 0.8275 (t0) REVERT: B 73 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7553 (mpt) REVERT: B 197 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: B 291 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8337 (tp-100) REVERT: B 432 GLU cc_start: 0.0792 (OUTLIER) cc_final: 0.0313 (pt0) outliers start: 39 outliers final: 28 residues processed: 102 average time/residue: 1.0787 time to fit residues: 120.0492 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 93 ILE 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 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 367 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.066094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051656 restraints weight = 30216.000| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.40 r_work: 0.2938 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9954 Z= 0.298 Angle : 0.665 12.456 13504 Z= 0.333 Chirality : 0.046 0.253 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.366 145.826 1475 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 3.69 % Allowed : 24.05 % 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: -0.12 (0.24), residues: 1221 helix: 1.50 (0.23), residues: 502 sheet: 0.05 (0.36), residues: 215 loop : -1.84 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.017 0.002 PHE A 149 TYR 0.014 0.002 TYR K 146 ARG 0.007 0.001 ARG K 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.46 seconds wall clock time: 101 minutes 39.43 seconds (6099.43 seconds total)