Starting phenix.real_space_refine on Fri Oct 10 23:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uts_42548/10_2025/8uts_42548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uts_42548/10_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_42548/10_2025/8uts_42548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uts_42548/10_2025/8uts_42548.map" model { file = "/net/cci-nas-00/data/ceres_data/8uts_42548/10_2025/8uts_42548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uts_42548/10_2025/8uts_42548.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.48, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 370.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.77 Time building geometry restraints manager: 1.24 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: 5.940 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (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 ARG 0.008 0.001 ARG A 214 TYR 0.051 0.002 TYR B 36 PHE 0.032 0.002 PHE A 267 TRP 0.024 0.002 TRP B 344 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9954) covalent geometry : angle 0.83571 (13504) hydrogen bonds : bond 0.16624 ( 460) hydrogen bonds : angle 6.13265 ( 1422) *********************** 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 : 0.434 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: 0.7036 (tpt170) REVERT: K 356 CYS cc_start: 0.3532 (OUTLIER) cc_final: 0.3308 (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: 0.7458 (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: 0.6073 time to fit residues: 133.9702 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 : 0.391 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 2.3942 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.069052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054605 restraints weight = 29225.059| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.47 r_work: 0.2993 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2079 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= 0.140 Angle : 0.634 9.000 13504 Z= 0.322 Chirality : 0.046 0.302 1483 Planarity : 0.005 0.095 1757 Dihedral : 13.510 147.747 1484 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.77 % Favored : 95.90 % Rotamer: Outliers : 3.88 % Allowed : 20.93 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.24), residues: 1221 helix: 1.74 (0.24), residues: 500 sheet: 0.21 (0.34), residues: 223 loop : -1.35 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 306 TYR 0.017 0.001 TYR K 146 PHE 0.013 0.001 PHE K 221 TRP 0.009 0.001 TRP A 21 HIS 0.017 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9954) covalent geometry : angle 0.63443 (13504) hydrogen bonds : bond 0.04346 ( 460) hydrogen bonds : angle 4.67731 ( 1422) *********************** 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 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 98 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8290 (mm110) REVERT: A 71 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 108 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.5347 (p90) REVERT: A 211 ASP cc_start: 0.8878 (m-30) cc_final: 0.8571 (t70) REVERT: A 239 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8855 (t) REVERT: A 432 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6555 (t80) REVERT: B 1 MET cc_start: 0.6926 (mmp) cc_final: 0.6703 (mmp) REVERT: B 209 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8778 (t0) REVERT: B 363 MET cc_start: 0.9072 (ptp) cc_final: 0.8741 (ptt) REVERT: B 432 GLU cc_start: 0.1517 (OUTLIER) cc_final: 0.1288 (tt0) outliers start: 41 outliers final: 10 residues processed: 132 average time/residue: 0.5188 time to fit residues: 74.4388 Evaluate side-chains 90 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 301 THR 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 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 209 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 SER 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 2 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 83 optimal weight: 0.0030 chunk 89 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 GLN A 192 HIS B 137 HIS B 165 ASN ** 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 = 0.3432 r_free = 0.3432 target = 0.067053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052378 restraints weight = 29790.768| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.44 r_work: 0.2943 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9954 Z= 0.190 Angle : 0.646 9.707 13504 Z= 0.328 Chirality : 0.047 0.421 1483 Planarity : 0.005 0.094 1757 Dihedral : 10.405 144.533 1478 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.34 % Favored : 95.41 % Rotamer: Outliers : 4.45 % Allowed : 20.93 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.24), residues: 1221 helix: 1.58 (0.23), residues: 510 sheet: 0.42 (0.36), residues: 215 loop : -1.45 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 264 TYR 0.015 0.002 TYR K 146 PHE 0.017 0.002 PHE A 149 TRP 0.010 0.001 TRP A 21 HIS 0.012 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9954) covalent geometry : angle 0.64603 (13504) hydrogen bonds : bond 0.04591 ( 460) hydrogen bonds : angle 4.63776 ( 1422) *********************** 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 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6136 (p90) REVERT: A 211 ASP cc_start: 0.8937 (m-30) cc_final: 0.8706 (t70) REVERT: A 239 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8815 (t) REVERT: A 432 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6476 (t80) REVERT: B 209 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8655 (t0) REVERT: B 291 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8340 (tp-100) REVERT: B 363 MET cc_start: 0.9077 (ptp) cc_final: 0.8699 (ptt) REVERT: B 432 GLU cc_start: 0.1281 (OUTLIER) cc_final: 0.0804 (pt0) outliers start: 47 outliers final: 16 residues processed: 122 average time/residue: 0.5572 time to fit residues: 73.5425 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 : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 229 ARG 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 239 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 0.0570 chunk 23 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN ** 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 = 0.066633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052053 restraints weight = 29924.813| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.42 r_work: 0.2939 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3308 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= 0.181 Angle : 0.624 9.501 13504 Z= 0.318 Chirality : 0.047 0.373 1483 Planarity : 0.005 0.089 1757 Dihedral : 9.323 144.011 1478 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 4.07 % Allowed : 21.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1221 helix: 1.64 (0.23), residues: 509 sheet: 0.46 (0.35), residues: 221 loop : -1.57 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 316 TYR 0.013 0.002 TYR K 146 PHE 0.018 0.002 PHE A 149 TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9954) covalent geometry : angle 0.62442 (13504) hydrogen bonds : bond 0.04376 ( 460) hydrogen bonds : angle 4.60934 ( 1422) *********************** 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 115 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 72 time to evaluate : 0.422 Fit side-chains REVERT: A 108 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.6510 (p90) REVERT: A 211 ASP cc_start: 0.8972 (m-30) cc_final: 0.8768 (t70) REVERT: A 367 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: A 432 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6609 (t80) REVERT: B 31 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: B 67 ASP cc_start: 0.8702 (t0) cc_final: 0.8347 (t0) REVERT: B 209 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8859 (t70) REVERT: B 311 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 363 MET cc_start: 0.9078 (ptp) cc_final: 0.8682 (ptt) REVERT: B 432 GLU cc_start: 0.0963 (OUTLIER) cc_final: 0.0334 (pt0) outliers start: 43 outliers final: 16 residues processed: 110 average time/residue: 0.5269 time to fit residues: 63.1200 Evaluate side-chains 85 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL 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 108 TYR Chi-restraints excluded: chain A residue 118 VAL 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 164 MET Chi-restraints excluded: chain B residue 178 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 0.0770 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 209 ASN B 131 GLN B 332 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 = 0.3436 r_free = 0.3436 target = 0.067233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.052673 restraints weight = 29676.724| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.41 r_work: 0.2957 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9954 Z= 0.136 Angle : 0.581 9.644 13504 Z= 0.295 Chirality : 0.045 0.260 1483 Planarity : 0.005 0.087 1757 Dihedral : 9.160 142.285 1478 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.59 % Favored : 95.25 % Rotamer: Outliers : 3.69 % Allowed : 21.88 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1221 helix: 1.78 (0.23), residues: 512 sheet: 0.48 (0.34), residues: 220 loop : -1.57 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 316 TYR 0.010 0.001 TYR A 108 PHE 0.017 0.001 PHE A 149 TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9954) covalent geometry : angle 0.58111 (13504) hydrogen bonds : bond 0.03948 ( 460) hydrogen bonds : angle 4.42758 ( 1422) *********************** 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 110 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 0.405 Fit side-chains REVERT: K 99 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8367 (t) REVERT: A 71 GLU cc_start: 0.7707 (tt0) cc_final: 0.7460 (tt0) REVERT: A 108 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.6487 (p90) REVERT: A 211 ASP cc_start: 0.8986 (m-30) cc_final: 0.8779 (t70) REVERT: A 230 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9089 (mt) REVERT: A 367 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: A 432 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6517 (t80) REVERT: B 31 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: B 67 ASP cc_start: 0.8676 (t0) cc_final: 0.8314 (t0) REVERT: B 209 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8868 (t70) REVERT: B 291 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8305 (tp-100) REVERT: B 432 GLU cc_start: 0.0720 (OUTLIER) cc_final: 0.0171 (pt0) outliers start: 39 outliers final: 17 residues processed: 106 average time/residue: 0.5221 time to fit residues: 60.3118 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL 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 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 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 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 164 MET Chi-restraints excluded: chain B residue 178 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 0.0270 chunk 14 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** 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 = 0.067036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052448 restraints weight = 29872.882| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.41 r_work: 0.2950 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9954 Z= 0.150 Angle : 0.585 10.597 13504 Z= 0.296 Chirality : 0.045 0.251 1483 Planarity : 0.005 0.085 1757 Dihedral : 9.149 141.766 1478 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 3.98 % Allowed : 22.54 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.24), residues: 1221 helix: 1.77 (0.23), residues: 512 sheet: 0.41 (0.34), residues: 220 loop : -1.60 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 316 TYR 0.027 0.001 TYR K 146 PHE 0.017 0.001 PHE A 149 TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9954) covalent geometry : angle 0.58507 (13504) hydrogen bonds : bond 0.04073 ( 460) hydrogen bonds : angle 4.45274 ( 1422) *********************** 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 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 0.404 Fit side-chains REVERT: K 99 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8364 (t) REVERT: A 230 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9076 (mt) REVERT: A 432 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6534 (t80) REVERT: B 31 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: B 67 ASP cc_start: 0.8720 (t0) cc_final: 0.8352 (t0) REVERT: B 209 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8852 (t70) REVERT: B 291 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8306 (tp-100) REVERT: B 311 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 432 GLU cc_start: 0.0853 (OUTLIER) cc_final: 0.0303 (pt0) outliers start: 42 outliers final: 20 residues processed: 102 average time/residue: 0.4966 time to fit residues: 55.3691 Evaluate side-chains 91 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 VAL 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 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 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 164 MET Chi-restraints excluded: chain B residue 178 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.0470 chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 overall best weight: 4.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 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 = 0.066581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052345 restraints weight = 29807.149| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.35 r_work: 0.2944 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9954 Z= 0.178 Angle : 0.617 10.641 13504 Z= 0.310 Chirality : 0.045 0.257 1483 Planarity : 0.005 0.085 1757 Dihedral : 9.260 141.855 1478 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 3.98 % Allowed : 22.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1221 helix: 1.73 (0.23), residues: 501 sheet: 0.30 (0.34), residues: 220 loop : -1.70 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 316 TYR 0.012 0.002 TYR A 172 PHE 0.018 0.002 PHE A 149 TRP 0.009 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9954) covalent geometry : angle 0.61708 (13504) hydrogen bonds : bond 0.04347 ( 460) hydrogen bonds : angle 4.53735 ( 1422) *********************** 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 106 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.412 Fit side-chains REVERT: K 107 MET cc_start: 0.8383 (mmt) cc_final: 0.8177 (tpp) REVERT: A 230 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9075 (mt) REVERT: A 432 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6561 (t80) REVERT: B 1 MET cc_start: 0.7316 (mmp) cc_final: 0.6971 (mmt) REVERT: B 31 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: B 67 ASP cc_start: 0.8766 (t0) cc_final: 0.8413 (t0) REVERT: B 209 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8834 (t70) REVERT: B 291 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8295 (tp-100) REVERT: B 432 GLU cc_start: 0.0860 (OUTLIER) cc_final: 0.0337 (pt0) outliers start: 42 outliers final: 23 residues processed: 102 average time/residue: 0.4900 time to fit residues: 54.6008 Evaluate side-chains 89 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 143 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 193 GLN ** 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 = 0.3417 r_free = 0.3417 target = 0.066236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051763 restraints weight = 30254.871| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.39 r_work: 0.2934 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9954 Z= 0.199 Angle : 0.635 11.427 13504 Z= 0.321 Chirality : 0.046 0.257 1483 Planarity : 0.005 0.086 1757 Dihedral : 9.350 144.115 1478 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 3.88 % Allowed : 22.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1221 helix: 1.58 (0.23), residues: 503 sheet: 0.23 (0.34), residues: 218 loop : -1.70 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 309 TYR 0.014 0.002 TYR A 172 PHE 0.019 0.002 PHE A 149 TRP 0.009 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9954) covalent geometry : angle 0.63482 (13504) hydrogen bonds : bond 0.04566 ( 460) hydrogen bonds : angle 4.63924 ( 1422) *********************** 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 106 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.406 Fit side-chains REVERT: K 107 MET cc_start: 0.8382 (mmt) cc_final: 0.8151 (tpp) REVERT: K 108 MET cc_start: 0.8460 (mmm) cc_final: 0.8132 (pp-130) REVERT: A 230 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9068 (mt) REVERT: A 367 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: A 432 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6556 (t80) REVERT: B 31 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: B 67 ASP cc_start: 0.8803 (t0) cc_final: 0.8458 (t0) REVERT: B 209 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8836 (t70) REVERT: B 291 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8323 (tp-100) REVERT: B 432 GLU cc_start: 0.0880 (OUTLIER) cc_final: 0.0446 (pt0) outliers start: 41 outliers final: 24 residues processed: 104 average time/residue: 0.5297 time to fit residues: 59.9537 Evaluate side-chains 91 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.067847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053527 restraints weight = 29697.435| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.35 r_work: 0.2983 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9954 Z= 0.109 Angle : 0.582 12.855 13504 Z= 0.285 Chirality : 0.044 0.238 1483 Planarity : 0.005 0.086 1757 Dihedral : 8.879 143.427 1476 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.75 % Favored : 95.09 % Rotamer: Outliers : 2.65 % Allowed : 23.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1221 helix: 1.89 (0.24), residues: 505 sheet: 0.44 (0.34), residues: 220 loop : -1.64 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 254 TYR 0.008 0.001 TYR K 146 PHE 0.016 0.001 PHE A 149 TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9954) covalent geometry : angle 0.58205 (13504) hydrogen bonds : bond 0.03574 ( 460) hydrogen bonds : angle 4.29596 ( 1422) *********************** 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 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.425 Fit side-chains REVERT: K 107 MET cc_start: 0.8388 (mmt) cc_final: 0.8187 (tpp) REVERT: K 108 MET cc_start: 0.8469 (mmm) cc_final: 0.8126 (pp-130) REVERT: K 230 HIS cc_start: 0.6643 (t70) cc_final: 0.6116 (OUTLIER) REVERT: K 288 MET cc_start: 0.8499 (mtt) cc_final: 0.8280 (tpp) REVERT: A 230 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9042 (mt) REVERT: A 432 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6493 (t80) REVERT: B 1 MET cc_start: 0.7220 (mmp) cc_final: 0.6761 (mmp) REVERT: B 31 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: B 67 ASP cc_start: 0.8707 (t0) cc_final: 0.8349 (t0) REVERT: B 164 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7641 (tpt) REVERT: B 432 GLU cc_start: 0.0751 (OUTLIER) cc_final: 0.0396 (pt0) outliers start: 28 outliers final: 17 residues processed: 93 average time/residue: 0.5524 time to fit residues: 55.5856 Evaluate side-chains 83 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 168 VAL Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain A residue 109 THR 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 164 MET Chi-restraints excluded: chain B residue 178 THR 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 18 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.066866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052595 restraints weight = 29532.823| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.31 r_work: 0.2960 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9954 Z= 0.171 Angle : 0.620 11.206 13504 Z= 0.310 Chirality : 0.045 0.254 1483 Planarity : 0.005 0.086 1757 Dihedral : 8.988 142.292 1474 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 2.65 % Allowed : 24.24 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.24), residues: 1221 helix: 1.77 (0.24), residues: 507 sheet: 0.47 (0.35), residues: 216 loop : -1.67 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 309 TYR 0.027 0.001 TYR K 146 PHE 0.017 0.001 PHE A 149 TRP 0.008 0.001 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9954) covalent geometry : angle 0.61982 (13504) hydrogen bonds : bond 0.04251 ( 460) hydrogen bonds : angle 4.47089 ( 1422) ********************** 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 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.484 Fit side-chains REVERT: K 107 MET cc_start: 0.8369 (mmt) cc_final: 0.8160 (tpp) REVERT: K 230 HIS cc_start: 0.6652 (t70) cc_final: 0.6128 (OUTLIER) REVERT: A 230 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9068 (mt) REVERT: A 432 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6580 (t80) REVERT: B 31 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: B 67 ASP cc_start: 0.8766 (t0) cc_final: 0.8422 (t0) REVERT: B 164 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7853 (tpp) REVERT: B 291 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8322 (tp-100) REVERT: B 432 GLU cc_start: 0.0910 (OUTLIER) cc_final: 0.0562 (pt0) outliers start: 28 outliers final: 19 residues processed: 93 average time/residue: 0.5268 time to fit residues: 53.3108 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 GLU Chi-restraints excluded: chain A residue 109 THR 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 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 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 99 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.067376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053108 restraints weight = 29884.152| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.35 r_work: 0.2973 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9954 Z= 0.136 Angle : 0.615 13.068 13504 Z= 0.302 Chirality : 0.044 0.246 1483 Planarity : 0.005 0.085 1757 Dihedral : 8.902 142.675 1474 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 2.56 % Allowed : 24.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.24), residues: 1221 helix: 1.83 (0.24), residues: 505 sheet: 0.54 (0.35), residues: 216 loop : -1.64 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 309 TYR 0.013 0.001 TYR K 146 PHE 0.018 0.001 PHE K 221 TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9954) covalent geometry : angle 0.61547 (13504) hydrogen bonds : bond 0.03937 ( 460) hydrogen bonds : angle 4.40638 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.93 seconds wall clock time: 52 minutes 9.17 seconds (3129.17 seconds total)